The video stream will be exactly the same as the MKV, so I'm definitely sticking with v2.5.
I don't see any reason for confusion (or additional confusion - there will be questions like "what's the difference between the MKV and the BD" either way). It will be the BD release of v2.5, and the v2.5 MKV is kind of like an iTunes or Netflix release - they are not different versions of the film, just different release formats.