CS-Hover,
You are close. Your explanation would be correct if the length and width of the tanks were the same and they only differed in depth. However, the aux tank is not only less deep than the main tank, but also shorter in the longitudinal axis, ie from the front of the tank to the back of the tank. I think it may also be narrower laterally, but I'm not certain.
So the excess volume is not just at the bottom of the main tank, it is also at the aft end of the tank. Here's a simple diagram with an aux tank (in black) overlaid inside a main tank (in blue), not to scale by any means:
If we were to remove the crossfeed tube so that the tanks' levels didn't automatically equalize, and then remove an equal amount of fuel from each tank, we would observe that the fuel level in the aux tank would decrease more than the fuel level in the main tank.
Hope this helps,
SS.