I suppose an option for this scenario would be:
If you have a given ship set which is to be used by a mod or mods, include the model geometry in a separate VP called up by the multimod feature in the .ini file. For instance, you might have "SteveOsCapShips.vp" which might contain the standard Raynor, Titan, etc. Then you might have a set of Shivan ships, "ShivanPack1.vp". And the list would continue...
The problem with this method is standardizing the naming conventions as well as the .vp contents. This could work, and the only things the mod itself would need to carry would be any unique textures and tables. Apart from that, though, there's nothing really worth while in something like that. Enough people new to FSO seem to be confused about what they need as is, and this would only make it harder on them, I imagine.
I think it's probably better things stay as-is for now. Of course, if you have a shortage of hard drive space, you could always do something like this for yourself...