If you want chapters, you need to use the MPLS, not the M2TS. And if your title has seamless branching (i.e The Martian that has Theatrical and Extended on the same disc), you either need to use the MPLS, or manually drag all of the M2TS files into MKVToolnix, in order, and choose to append them.
And yes, no Dolby Vision in MKV - the MKVToolnix 17.0 release thread (https://forum.doom9.org/showthread.php?p=1821281) has discussion on that.
I do agree that I prefer MakeMKV for forced sub handling, but luckily of the one UHD I have that has forced subs, the disc already had a separate sub track with the forced subs. I also prefer its track auto-selection (for me, english only, lossless audio, no core audio).