3D-MKV is compatible with Matroska, but the MVC is hidden.
You can remux the 3D output from MakeMKV with MKVtoolnix, the MVC is retained. But MKVmerge is not able to generate new 3D-MKVs from AVC and MVC.
The only player for 3D-MKV is the Stereoscopic Player from Peter Wimmer. 3D-subs are not well supported.
You can generate a simple 3D-Blu-ray from 3D-MKV with tsMuxeR to play on 3D standard players.
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