I think the issue is offiucally MKV supports 3d via mk3d, which isn't for MVC but stereo like SBS. So it has no field to put the first eye in for MVC. So MakeMKV could see the data in the iso, but has nowhere to put it.
Since using TAB off the menu triggers MVC processing.....it might be possible to remux MKV to mkv3d stating its TAB, and which is first Top or bottom. It could just create an unplayable file.
Did you have the problem with the iso as well?