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What determines the chapter or video length? Is it the number of frames divided by fps or some time marker in the audio?
I found some information about mpls structure. Time offsets and durations are measured in 45000ths of a second. There is no relation to video or audio.
I still think that ...

mpls file contains full information about chapters. No matter what number of m2ts files it has.

the director didn't worry about chapter break points while filming the movie
That's smart excuse :)

MakeMKV has the feature and it must works well with same accuracy like in audio and subtitles. This is my point.

Chapters can be truncated to 3 digits after point like MediaInfo shows if ...

Every Blu-ray and UHD Blu-ray I tested converts to mkv with inaccurate timestamps in chapters. Deviation is about 100-400 milliseconds in almost all chapters. Can this be fixed?

Some examples:

Blade Runner 2049 UHD Blu-ray

00020.mpls, chapters in MediaInfo:
00:00:00.000 : Chapter 1
00:12:50 ...