Fortunately, that necro brought it back to my attention as I'd been rather busy.
At a root level, FSU is (as noted earlier) intended to be an assets and visual upgrade to Retail. End of story.
Mods that Work: Any mod that has, say, a Myrmidon vs. Ulysses where they haven't tabled or textured anything fancy, they just want two ships/wings having a dog-fight. Regardless of MediaVPs version, that will always work and be "the latest" that the user has installed (or Retail if run with no mods).
Mods that Break: Same as the mod above, but now they've elected to change the glowmaps or textures or utilize team-colors, but they ONLY applied their changed maps and tbm edits into the mod. So if either of those two models get remade or remapped in the MediaVPs, they will now no longer work as intended in the mod because things will no longer be in alignment.
It'd be much easier for the mod to maintain its own model for such significant changes. At the very least, when such a breakage occurs (and model changes like that always have a thread or are announced (or will/should be) in the changelog), grab the previous model at THAT point in time as an over-ride compatibility patch for the mod to use until it can adapt to using the newer model. Assuming there hasn't already been enough of a community awareness that the relevant re-textures to upgrade the mod aren't already done. But it would be a change cycle that would have to be completely re-iterated on with each release one way or the other (either by including the model to go with the texture changes and bulk wholesale updating them later, or updating the textures each time the model changes).
Or reference that the mod is compatible with a version that maintains the intended behaviour.