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.
If it were from a nacelle it would have come and gone since the nacelle is much thinner toward the back and the light source is coming from the top right, it starts when the shuttle enters the bay and doesn't stop. The shadow itself is caused by the structure of the landing bay. The Vengeance itself goes from a semi blurry looking dreadnought to a detailed dreadnought as it's hitting the water. I'm pretty sure that the shadow is coming from edge of the shuttlebay though because as we see the shuttle go further and the shadow continues being cast on the shuttle as it enters the bay. The entering shuttle is also larger than the one superimposed inside the bay itself that daniel highlighted earlier. We saw the new smaller shuttlebay when the enterprise lost power and fell to earth, kirk and scotty saw a few shuttles fall off of their plateforms and behind them was the door itself highlighted with soft white light bars.