Yes. Generally there is a lot of scaling and then individual ScreenGraphNodes get jostled around to fit, more or less, where they are supposed to go. On the last model I went a little overboard, I even had the inlet compressor animations shrunk down and stuffed into the intakes of my model. It seems like all the added transformations put a strain on the software. If you want to test it, the fastest path I've discovered so far, is that HPG AIrbus, all I had to do, was delete a few nodes in the Hierarchy Editor and MCX locked the model. Otherwise, the 787 and 747 animations are the most complex, maybe try shrinking the 747 animations into a BAE-146.
Also, the F-18E animations breaks almost immediately, it is the reason I could not use the front wheel animation from the Hornet. I am pretty sure this distortion happens upon import - or it's remotely possible the Hornet animation is broken this badly, that had been my initial reaction, when I discovered that MCX will actually "drop" or ignore animations. Anyway, all I had to do to get this far, was isolate the top ScreenGraphNode of the animations and then zoom in for these images.
You can see that the lower half of the oleo, or suspended part of the gear has become detached and sits to the side of it's assembly. If you cycle the animation, you can see that it circles its "parent," while the main suspension cycles it's compression phase. It seems pretty clear that that linear compression motion, has been transformed into a rotational motion. I feel like, if I just knew the transformation panel better, maybe using the matrix section, I could repair it.
Here's another view of that bogie after its finished circling and it ends up visibly off center alongside the part it is supposed to rest within. This should be an easy test to run and granted, it does not cause MCX to refuse the export, but I see that transition to just be an extension of this glitch. It starts with missed, or distorted animations and escalates until the ".mdl based animations" flag is thrown to end the play.
I've attached the same set of animations, one has been frozen by MCX for specious violations. You could try bending the working one, to fit the shape of the frozen one, maybe.
That Virtavia Tu-16 ended up being rotten to the core, btw. I went so far as to remove all animations, I exported it to Collada, then from the Collada to glTF to try to cleanse it of it's FSX taint, nothing helped. If I tried to build it as an empty hulk, if I tried to build the default animations with it removed, there was no problem, no warnings or errors, but the moment I selected it, MSFS would CTD. So, even if MCX had allowed the default animations, the model was already doomed from the start. I have a different model to try with next.