The best way, I found to make an MKV from a BD with multiple crawl, or seemless branching in general (tested with the official BDs, not this but I’d assume it would be the same) is to import not the m2ts files into the muxing program, but the playlist file corresponding to the version you want.
That’s true, but Makemkv does a better job at joining multiple M2TS files than mkvtoolnix in my experience. Mkvtoolnix gives some error frames at joined points sometimes for some reason (I’m pretty sure it did this on one of my Alien discs, so now I only use MakeMKV to convert .MPLS to .MKV).
I usually join using TSMuxer v1.12 (versions 2.xx don’t work as well for this) before using mkvtoolnix. That eliminates the errors.