www.makemkv.com

I haven't ripped the TV show Chuck (2007).

It is really dependent on the show. Most TV shows I've ripped, each episode is its own title on the disc. Usually the hardest part is sorting out which episode is which so as to name them properly. Not all TV shows seem to put the episodes on disc in order and MakeMKV sometimes displays them in a jumble.

I personally haven't encountered a show that only puts everything into one giant 'playall' title and indexes episodes into it at chapter markers, but I seem to recall others mentioning discs like that. Sometimes on shows on DVDs, I've seen both individual episode titles as well as one giant title of everything on the disc, the 'playall' title.

At the end of the day, there are no standards or requirements. And as soon as you think you understand the convention, you'll encounter a disc authored in a way that upends convention. This is why my workflow is to make a decrypted backup of the disc then make .mkv files from the backup.

Chuck is a tough one (great show, though). Some of the disks have individual episodes, some have all the episodes in one large file that needs to be split. You're on the right track with MKVToolNix. You can split by chapter and get nice clean results.

Also, as @dcoke22 said, they are definitely not in sequential order by file name. You will need to sort out which episode is which.... took me quite a while.

Here are the episode lengths to the second. This may help you sort out the mess:
https://thetvdb.com/series/chuck#seasons

S01E01 - 43:15
S01E02 - 42:50
S01E03 - 43:16
S01E04 - 43:13
S01E05 - 43:13
S01E06 - 41:15
S01E07 - 42:12
S01E08 - 43:17
S01E09 - 43:14
S01E10 - 42:44 <-- my blu ray was defective so I pulled this episode from DVD (temporarily)
S01E11 - 42:32
S01E12 - 43:17
S01E13 - 42:33

S02E01 - 43:21
S02E02 - 43:17
S02E03 - 43:17
S02E04 - 43:19
S02E05 - 43:18
S02E06 - 43:20
S02E07 - 42:01
S02E08 - 42:58
S02E09 - 43:02
S02E10 - 43:03
S02E11 - 43:00
S02E12 - 42:50
S02E13 - 43:00
S02E14 - 43:01
S02E15 - 43:00
S02E16 - 43:02
S02E17 - 43:00
S02E18 - 43:03
S02E19 - 43:02
S02E20 - 43:02
S02E21 - 43:02
S02E22 - 43:04

S03E01 - 43:03
S03E02 - 42:18
S03E03 - 43:05
S03E04 - 43:00
S03E05 - 43:01
S03E06 - 43:04
S03E07 - 43:06
S03E08 - 42:24
S03E09 - 43:06
S03E10 - 43:03
S03E11 - 43:02
S03E12 - 43:03
S03E13 - 43:03
S03E14 - 43:02
S03E15 - 43:02
S03E16 - 43:03
S03E17 - 43:03
S03E18 - 37:21 <-- an oddly shorter episode - could be a rip error on my end
S03E19 - 43:04

S04E01 - 43:02
S04E02 - 43:02
S04E03 - 43:02
S04E04 - 43:01
S04E05 - 43:00
S04E06 - 43:03
S04E07 - 43:02
S04E08 - 43:02
S04E09 - 43:05
S04E10 - 43:07
S04E11 - 43:05
S04E12 - 43:05
S04E13 - 43:02
S04E14 - 42.57
S04E15 - 43:03
S04E16 - 43:03
S04E17 - 43:03
S04E18 - 43:01
S04E19 - 43:01
S04E20 - 43:02
S04E21 - 43:02
S04E22 - 43:03
S04E23 - 43:04
S04E24 - 43:05

S05E01 - 43:17
S05E02 - 43:18
S05E03 - 43:19
S05E04 - 43:18
S05E05 - 43:16
S05E06 - 43:17
S05E07 - 43:18
S05E08 - 43:18
S05E09 - 43:17
S05E10 - 43:17
S05E11 - 43:14
S05E12 - 43:19
S05E13 (extended version) - 53:03