I got one of these obfuscated disks from the library and have been playing around with it. The disc is "You Were Never Really Here", and if I open it on my PC with VLC to play it it always opens Title 33. It's not one of the disks that really messes with you by playing a different title each time, but it does have 30 VTS'es with many having the same total movie time. When I originally posted I wanted to know how you figure out what title goes with what VTS, and I think I figured out how to determine that (and rip the correct movie).
When you first open MKV and select File/Open Disc it will give the output below and try to figure out all the real chapters (notice near the end that title 33 - the one VLC will always pick - has a total time of 1:29:48). For this disc it found 10 possible valid titles out of 34. It then lists all those titles with a checked box in front so you can rip them all if want (I did just to show the output below). But out of the 10 it found, only 6 have 16 chapters and a reasonable total size (those 4 that don't have 16 chapters can be unchecked). Then you can select / click on each of the remaining 6 and on the right hand pane it gives "Title Information", and one of those items is "Duration". After clicking through all six I find that only one has a duration of 1:29:48 (title06.mkv) that matches the Title 33 total time I mentioned above. Looks like that is probably our movie, so uncheck all but that one. While MakeMKV is ripping the title it will put the source file VTS it is using in the information window (in this case VTS_19).
As I said I ripped all six just to make sure. Once all the files are ripped you can see in the 2nd log file that 1 of the 6 (title04.mkv) failed to save, and then all the files that were saved except for 1 (title06.mkv) had this error "AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title0x.mkv'". So looks like title06.mkv really is the right file. To verify you can open up two instances of VLC and play the original DVD in one, and title06.mkv in the other. Then use playback/chapter or playback/jump to specific time to make sure the video lines up.
Another great enhancement to MakeMKV would be when it lists the 10 possible valid titles that it gives the actual title! Currently it just has all 10 and they are called just "Title". And if the source VTS could also be put here (or in the Title Information pane) another big plus.
Anyways hope this helps. I plan to get Chappaquiddick and Wonder from the library just to test out a few more of these disks to make sure this process works for more than this DVD.
-----------------------------Start Output from File/OpenDisc----------------------------
MakeMKV v1.12.2 win(x64-release) started
The new version 1.12.3 is available for download at
http://www.makemkv.com/download/
Using direct disc access mode
Manual String parse error : string is empty
Failed to open disc
Using direct disc access mode
Title #1 has length of 37 seconds which is less than minimum title length of 120 seconds and was therefore skipped
Title #2 has length of 30 seconds which is less than minimum title length of 120 seconds and was therefore skipped
Cells 2-4 were skipped due to cell commands (structure protection?)
Title #5 was added (16 cell(s), 1:27:15)
Title #6 was added (3 cell(s), 0:05:32)
Title #15 has length of 5 seconds which is less than minimum title length of 120 seconds and was therefore skipped
Title #16 was added (1 cell(s), 0:16:45)
Title #17 was added (1 cell(s), 0:17:45)
Title #20 was added (18 cell(s), 1:32:45)
Cells 2-4 were skipped due to cell commands (structure protection?)
Title #21 was added (16 cell(s), 1:27:52)
CellWalk algorithm failed (structure protection is too tough?), trying CellTrim algorithm
Cells 1-1 were removed from title start
Cells 18-18 were removed from title end
Title #22 was added (16 cell(s), 1:29:48)
Cells 2-4 were skipped due to cell commands (structure protection?)
Title #24 was added (16 cell(s), 1:27:18)
Cells 2-4 were skipped due to cell commands (structure protection?)
Title #25 was added (16 cell(s), 1:27:51)
CellWalk algorithm failed (structure protection is too tough?), trying CellTrim algorithm
Cells 1-1 were removed from title start
Cells 18-18 were removed from title end
Title #26 was added (16 cell(s), 1:29:48)
CellWalk algorithm failed (structure protection is too tough?), trying CellTrim algorithm
Cells 1-1 were removed from title start
Cells 18-18 were removed from title end
Title #27 was added (16 cell(s), 1:29:48)
Title #28/0/2 was added (1 cell(s), 0:07:13)
Title #29 was added (18 cell(s), 1:32:45)
CellWalk algorithm failed (structure protection is too tough?), trying CellTrim algorithm
Cells 1-1 were removed from title start
Cells 18-18 were removed from title end
Title #30 was added (16 cell(s), 1:29:48)
Title #31 was added (18 cell(s), 1:32:45)
Title #32 was added (18 cell(s), 1:32:45)
CellWalk algorithm failed (structure protection is too tough?), trying CellTrim algorithm
Cells 1-1 were removed from title start
Cells 18-18 were removed from title end
Title #33 was added (16 cell(s), 1:29:48)
Title #34 was added (18 cell(s), 1:32:45)
Title 1 in VTS 17 is equal to title 1 and was skipped
Title 1 in VTS 17 is equal to title 1 and was skipped
Title 1 in VTS 17 is equal to title 1 and was skipped
Title 2 in VTS 17 is equal to title 1 and was skipped
Title 1 in VTS 19 is equal to title 1 and was skipped
Title 1 in VTS 19 is equal to title 1 and was skipped
Title 1 in VTS 19 is equal to title 1 and was skipped
Title 1 in VTS 19 is equal to title 1 and was skipped
Operation successfully completed
-----------------------------End Output from File/OpenDisc----------------------------
-----------------------------Start Output from Ripping----------------------------
Saving 6 titles into directory E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816
AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title00.mkv' (title #1)
AV sync issue in stream 0 at 0:04:40.947 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:41.531 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:43.483 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:44.033 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:45.485 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:46.035 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:46.986 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:47.537 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:47.987 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:49.038 : video frame timecode differs by +152.485s
AV sync issue in stream 0 at 0:04:49.038 : too many video frames with invalid timecodes, future messages will be suppressed
AV sync issue in stream 1 at 0:04:40.736 with duration of 1360.78ms : audio gap - 42.524 missing frame(s)
AV sync issue in stream 0 at 1:27:23.004 : video stream has 10169 frames with invalid timecodes
AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title04.mkv' (title #5)
AV sync issue in stream 0 at 1:29:55.490 : video frame timecode differs by -16.688ms
AV sync issue in stream 1 at 1:29:55.488 with duration of 777.778ms : audio gap - 24.305 missing frame(s)
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'OS error - STATUS_DEVICE_DATA_ERROR' occurred while reading '\Device\CdRom0' at offset '3754733568'
Error 'OS error - STATUS_DEVICE_DATA_ERROR' occurred while reading '\Device\CdRom0' at offset '3754733568'
Error 'OS error - STATUS_DEVICE_DATA_ERROR' occurred while reading '\Device\CdRom0' at offset '3754733568'
Error 'OS error - STATUS_DEVICE_DATA_ERROR' occurred while reading '\Device\CdRom0' at offset '3754733568'
Error 'OS error - STATUS_DEVICE_DATA_ERROR' occurred while reading '\Device\CdRom0' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Error 'Scsi error - MEDIUM ERROR:UNRECOVERED READ ERROR' occurred while reading '/VIDEO_TS/VTS_17_1.VOB' at offset '3754733568'
Failed to save title 4 to file E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title04.mkv
AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title05.mkv' (title #6)
AV sync issue in stream 0 at 0:05:17.433 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:18.017 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:19.969 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:20.520 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:21.971 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:22.522 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:23.473 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:24.023 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:24.474 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:25.525 : video frame timecode differs by +115.999s
AV sync issue in stream 0 at 0:05:25.525 : too many video frames with invalid timecodes, future messages will be suppressed
AV sync issue in stream 1 at 0:05:17.216 with duration of 672.174ms : audio gap - 21.005 missing frame(s)
AV sync issue in stream 0 at 1:27:59.490 : video stream has 10169 frames with invalid timecodes
AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title07.mkv' (title #8)
AV sync issue in stream 0 at 0:04:43.950 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:44.534 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:46.486 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:47.036 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:48.488 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:49.038 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:49.989 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:50.540 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:50.990 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:52.041 : video frame timecode differs by +149.482s
AV sync issue in stream 0 at 0:04:52.041 : too many video frames with invalid timecodes, future messages will be suppressed
AV sync issue in stream 1 at 0:04:43.776 with duration of 2297.601ms : audio gap - 71.8 missing frame(s)
AV sync issue in stream 0 at 1:27:26.007 : video stream has 10169 frames with invalid timecodes
AV synchronization issues were found in file 'E:/Video/_YOU_WERE_NEVER_REALLY_HERE_3816/title08.mkv' (title #9)
AV sync issue in stream 0 at 0:05:16.933 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:17.517 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:19.469 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:20.019 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:21.471 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:22.021 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:22.972 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:23.523 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:23.973 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:25.024 : video frame timecode differs by +116.499s
AV sync issue in stream 0 at 0:05:25.024 : too many video frames with invalid timecodes, future messages will be suppressed
AV sync issue in stream 1 at 0:05:16.736 with duration of 1152.174ms : audio gap - 36.005 missing frame(s)
AV sync issue in stream 0 at 1:27:58.990 : video stream has 10169 frames with invalid timecodes
Encountered 11 errors of type 'Read Error' - see
http://www.makemkv.com/errors/dvdread/
5 titles saved, 1 failed
-----------------------------End Output from Ripping----------------------------