I recently received the official case for the Raspberry Pi 3, and because of the changes made on the inside, HATs will not fit inside the case. This is not just because of the GPIO header, which I had previously addressed, but the clips on the inside of the front (side with the LEDs) of the case.
I'm confused why the Raspberry Pi Foundation would make them incompatible. Was this an accident, or are the use of HATs inside cases officially discouraged? I'm also rather disappointed, because I assumed any changes made would be to make the case MORE compatible, not LESS!