www.makemkv.com

I have https://bongda24h.vn/ Blu-ray that MakeMKV can read and rip however there is no chapter list to break out the unwanted material or episodes. Total MKV ends up being 46GB.
It does discover 28 chapters so I'm confused as to why they can't be selected individually?

Post-processing with mkvtoolnix or handbrake will allow you to split on chapter boundaries, but no, MakeMKV cannot do this on BDs.

It is possible to manually open DVDs, though, and create "titles" that contain only certain ranges of chapters. That is covered here: /manualdvd/