Oh well, if it isn't possible to have that "magnifying ship"- effect, let's have a pseudo-one.
How'bout this: The ship doesn't start to emerge immediately, but instead there could be a growing dark thingy in the middle of the vortex, but only when looking in from the frontside. The dark blob (it wouldn't need to be particularly ship-sized to produce a relatively nice effect) would increase swiftly in size, representing the front silhuette of incoming ship. After it reaches some sixe, the real ship starts to emerge from certain level... uh, this is difficult to explain in words, let me draw a picture:

So that when the frontal silhuette of the ship grows onto the size where it equals the ship's real frontal silhuette, the real ship model starts emerging from that level.
Only thing is, the dark silhuette should only be visible from inside the vortex model. That way it would create an illusion (on some level at least) that the vortex is really leading somewhere, and the ship comes from there. Right now it'd be all the same if the ship just emerged from perfectly flat cloud.
I even think that the same dark blob could be used for any ship. The animation could be relatively fast, lasting about half a second or perhaps two seconds at most (for really huge ships), from a single dark pixel at the center of vortex, to full-sized vessel silhuette.
What do you think? I think all it needs is another texture at another side of the vortex model, that's all.