RipIt4Me, also discontinued but still can be downloaded, was a frontend to DVD Decrypter and DVDShrink.
It 'parsed' the .IFO files, pretty much the same way that a user would navigate the menus, and fed the result to DVD Decrypter to remove VOBs that weren't called, 'empty' VOBs, menu tricks, etc used by the manufacturers to complicate copying.
It was the first program to do so, then, IIRC, DVD Fab picked up on the same modus operandi.
I don't think I found a DVD it couldn't handle.
DVD43 worked pretty well for what it did, transparent decryption, but I think it sometimes had problems with some DVDs. I haven't used it since Win7 days so no idea whether it still works, if it did then it's just a matter of opening the DVDs directly with HandBrake/VidCoder.
As for VidCoder, just drop the MKV on the interface, choose a preset under Builtin->General if there's one that matches framerate/dimensions, if there is multiple audio tracks or subs, select the ones you want to keep, then hit encode and see what the output is like. If you need more quality you can pick another preset or tweak the video encoding settings, (it uses HandBrake cli as the encoding engine).