Actually, as the guy doing most of the source coding for the Robotech mod, I can say that the answer to Bobboau's question is an emphatic "YES!"
There is no reason why the transformation cannot be animated by replacing a series of models quickly.
Basically, all that would be needed is the specific frames of the animation converted into individual models (being careful to maintain the correct origin point so the ship doesn't "wobble"...).
Then, the easiest method would be to add a function in either the rendering code or the ship code (with a corresponding "transforming" flag, which I've already coded into the mod) that generates a timestamp. When the timestamp has been reached, the code would change the pof file to the next model in the sequence. Of course, I haven't tried this out in practice, but the theory is sound and fits what I already know about the source code. The worst case scenario (if that process just would not work for some reason) would lead to the need to make each step in the transformation it's own ship (not difficult, but could be a problem if you have a large number of total ships or many total transforming ships).
I haven't tried it out for the Robotech mod yet because I don't have the pof files for the animations, but we're working on it.
As for the source code itself, I release it with each build of the new Robotech executable, so when I have successfully coded the transformation animations, I will release the source to everyone.
As for the actual transformations from one ship to another (without animations in between), as venom2506 said, that's already working just fine in the mod (and with new key commands in the game and complete SEXP support for it)
...
