It really wouldn't be that hard to compare what you received from the foundry with the masks you sent them. There are services that decap ICs and attempt to reverse engineer them. Here's the first hit I found on Google: http://www.intelligservices.com/Services.htm

You wouldn't need the reverse engineering. All you would need to do is to compare that all the metal layers (and perhaps poly) match what you sent. That's an almost trivial comparison. The hard part of reverse engineering is in figuring out what the circuitry actually does, and you already know that, since it's your chip!

It could be possible for a fab to alter diffusion layers to change the functionality of a chip. That would be harder to detect by services such as the one I mentioned. But it would be very hard, very time consuming, to attempt to hack in a backdoor by only messing with base layers, rather than messing with metal or with poly (where changes are easily observed).

If there were to be a backdoor anywhere in a design, it would be in IP you used on your chip, that you got from either your foundry or from a 3rd party IP supplier. It would be easy enough to hide all kinds of stuff there.