I've pretty much been lightly on your side with this, especially the monster ship crash in the bay, but on the shuttle deal, I am kinda thinking the shadow you mention -- which is most definitely there -- might be coming from the nacelle or some other object.
It looks like the shadow aspect occurs before the shuttle gets where it is supposed to be (then again, it could just be a lousy comp, in which case we again have ILM to blame, even if it is for a different reason this time.)
None of this changes the likelihood that the ship is getting resized as needed, since ILM has been doing this kind of thing for just about ever and ever (one model for Vermithrax in DRAGONSLAYER for flying and another for walking, and I'm pretty sure different CG models for DRAGONHEART's Draco, because there were interpenetration problems trying to get the wings to work while retaining the walking version of him. The Bird of Prey in SFS seems to change drastically in size from scene to scene, and I think the same can be said for TVH, though probably not so extreme a change.)
The bay shot MIGHT have been done with 'long' virtual lenses, suggesting more of a telephoto view, which would compress the field of view and distort the size of objects. Would have to look at a high rez version of the shot.