I use MAKEMKV exclusively for ripping Blu Rays, never a problem.
Assuming the Blu Ray has a variety of listening choices, stereo, 5.1, ATMOS, just to keep my answer simple.
It rips as what I call the root file, which is the MKV file.
Then I use Music Media Helper to select the 5.1 or stereo into FLAC lossless chapters, or tracks as you might call them, then tag and listen, very simple.
As my only goal is to get whatever I play, to play via JRiver player.
The Atmos lossless file, I split into MKV file chapters assuming it is not a gapless album as as of this writing JRiver will not playback gapless MKV chapters, it will playback FLAC gapless albums.
So my workaround, for instance Abbey Road/Beatles, I just include the root MKV file, and being that it also has the video with it, I can see name of song while I am listening if I choose to have screen on.
Between my rig, JRiver, MakeMKV and Music Media Helper, I get to listen to the highest available ripped source and I rarely have a listening problem, when I do, it is always a mistake I made.