www.makemkv.com

This is an original DVD in a 20 disc box set, the only one that MakeMKV cant read, makemkv fails about 3/4 of the way through. Both Eac3to and MKVMerge detect a problem but fix it and the resulting MKV is fine.

Here is the MKVMerge warning (Occurs where MakeMKV halts):
Warning: 'C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_0.VOB' track 1: This AC3 track contains 1344 bytes of non-AC3 data which were skipped. The audio/video synchronization may have been lost.
Warning: Shortened GOP detected. Some frames have been dropped. You may want to fix the MPEG2 video stream before attempting to multiplex it.
Warning: Shortened GOP detected. Some frames have been dropped. You may want to fix the MPEG2 video stream before attempting to multiplex it.
Warning: Shortened GOP detected. Some frames have been dropped. You may want to fix the MPEG2 video stream before attempting to multiplex it.
Warning: Shortened GOP detected. Some frames have been dropped. You may want to fix the MPEG2 video stream before attempting to multiplex it.
Warning: Shortened GOP detected. Some frames have been dropped. You may want to fix the MPEG2 video stream before attempting to multiplex it.

Is there any chance MakeMKV could be reislient to this problem as well?

What EAC3TO says but again the resulting file works fine:
eac3to v3.24
command line: eac3to C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_0.VOB+C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_1.VOB+C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_2.VOB+C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_3.VOB+C:\GUNDAM_X_VOL6\VIDEO_TS\VTS_01_4.VOB out.mkv
------------------------------------------------------------------------------
VOB, 1 video track, 1 audio track, 2 subtitle tracks, 0:48:45
1: Joined VOB file
2: MPEG2, 480i60 /1.001 (4:3)
3: AC3, 2.0 channels, 448kbps, 48kHz, dialnorm: -27dB
4: Subtitle (DVD)
5: Subtitle (DVD)
[v02] Extracting video track number 2...
[a03] Extracting audio track number 3...
[s04] Extracting subtitle track number 4...
[v02] Muxing video to Matroska...
[a03] Removing AC3 dialog normalization...
[a03] Creating file "out - 3 - AC3, 2.0 channels, 448kbps, 48kHz.ac3"...
[s05] Extracting subtitle track number 5...
[s04] Creating file "out - 4 - Subtitle (DVD).sup"...
[s05] Creating file "out - 5 - Subtitle (DVD).sup"...
[s05] This EVO/VOB file contains authoring faults. Will try to work around that. (2034) <WARNING>
[a03] This track is not clean. <WARNING>
[v02] Video overlaps for 13972 frames at playtime 0:00:33. <WARNING>
[v02] Video overlaps for 14 frames at playtime 0:00:37. <WARNING>
[v02] Video overlaps for 1938 frames at playtime 0:00:38. <WARNING>
[v02] Video overlaps for 7 frames at playtime 0:41:44. <WARNING>
[v02] The MKV file was created without making use of the gap/overlap information. <WARNING>
[v02] Please check whether audio is in sync. If it is in sync everything is fine. <WARNING>
[v02] Otherwise ask eac3to to repeat the muxing. It will then automatically make <WARNING>
[v02] use of the detailed gap/overlap information. <WARNING>
[a03] Audio overlaps for 33024ms at playtime 0:00:00. <WARNING>
[a03] Audio overlaps for 4544ms at playtime 0:00:00. <WARNING>
[a03] Starting 2nd pass...
[a03] Creating file "out - 3 - AC3, 2.0 channels, 448kbps, 48kHz.ac3"...
Added fps value (30 /1.001) to MKV header.
Video track 2 contains 71518 frames.
Subtitle track 4 contains 495 captions.
Subtitle track 5 contains 492 captions.
eac3to processing took 1 minute, 32 seconds.
Done.

I understand it is a matter of opinion but my own opinion is that as long as the user is clearly warned I dont see issue in "patching" minor errors.

Please send the full debug log per http://www.makemkv.com/faq/item/8/catid/6 if you haven't done so.