[HELP] Rename tracks help please and help with chapters

[Selur]

Nope, I simply added some chapters manually like I wrote.
Chapter file can't cause a fix-up or missing streams.
(broken chapter file might cause problems during playback and muxing, but that's about it)

What's wrong with .mp4 files?

mp4 container is fine (not suited for most audio streams on Blu-rays but fine).

I have a lot of movies, and .mp4 seems to have a lot more universal compatibility than .mkv.

Definitely not the .mkv container allows way more stuff than the mp4 container.

Would it be better to not have VFR?

Yes! Since your source isn't vfr, I see no good reason why one would create vfr unless one does a lot of filtering on anime content and too much time. For natural content, which was properly mastered once there should be no reason to use vfr.
-> Going from cfr to vfr is normally a stupid thing.

Cu Selur