This has been my experience with DVDs anyway: I have not used MakeMKV with any BluRays, so your claim of it carrying the BD menu structure over into the MKV file is quite surprising to me. These are played by software like VLC as if they were actual physical discs, retaining all the menu navigation and options that are normally lost when you 'rip to MKV'. This results in one big file, either as a folder or whole-disc image. The other type of 'ripping' used to be far more common than the MakeMKV method: you copy the entire disc structure, including all formatting, to your hard drive. Generally you would need to use another utility to divide this into individual eps. MakeMKV usually cannot parse this properly because it ignores menu data: all it sees is the one huge video file, so it dutifully creates one big MKV containing all the episodes. But some discs employ a more peculiar format of having all the episodes as one big chunk, like a VHS tape, relying on the disc menu navigation structure to select an episode. Most TV discs have the individual episodes loaded as separate pieces: Make MKV will recognize this and create individual MKV files for each.

MakeMKV does not alter the quality in any way but it does strip away the disc-specific formatting, which usually includes menu navigation and may include separation of episodes in a TV series depending how the original disc itself is authored. When using MakeMKV to rip from disc into MKV format, you're actually 'converting' from the disc structure to MKV file structure. You're mixing together what are usually two separate types of disc>file 'ripping' methods.

Makemkv dvd ripping