Because the FSPort files are designed to be retail compatible. FSPort MVPs are not.
As for interfacing with other mod files, well, it would behave just like FS2 campaigns; you would either need to edit their mod.ini to specify the FSPortMVP folder, or make an updated version specifically for the MVP (just like the Campaign Restoration Project did with Derelict.)
Alternatively you can just plop the VP into your main FSport folder and forget about it. But that's at your own risk as then bug reports can't be reliably disentangled.