I have overlaid an outline of the Raspberry Pi's shape (complete with mounting hole positions) on top of the current Dexter rev3 layout. I'm glad I did this because I think it needs to be moved around a little bit.
I am inclined to move the pin headers that connect to the pi up toward the top of the board. And just to be clear, I don't plan on encouraging people to mount the Pi to the Dexter board because there isn't going to be enough clearance. But if some clever person figures out a better way to do it later, I want the mounting holes to be there just in case.