I have to analyse the possibilities of MakeMkv. But if it's only the latest version that can do that, I will not be able to use it, for the reason highlighted by Frank
here. (I may change later the format of the MUX_OPTIONS files to be compatible with Mkvtoolnix v20+, but it's not currently in my todo list.)
Also, since you want to just remux the ORIGINAL AVC + MVC streams as a (big) MK3D, you can already use MakeMKV for that job. It does that very well, and it is still free if you use the key offered regularly
here. Just add the MVC stream in the list of streams to mux (as it is disabled by default) and let it do its job.
So, if I implement AVC+MVC support in BD3D2MK3D, it should be with the possibility to re-encode the AVC and MVC streams. But that's a big job, so don't expect that soon! And note that only a few Windows players support that format. I'm not really interested in implementing it while no standalone player or TV can play it.