Actually, it's quite a bit more than just being upside-down. One, the processor is toward the middle of the mobo, rather than closer to the top. The proc is also relocated to the front edge of the mobo, closer to the intake fans, rather than toward the rear as on ATX boards.
The PCIe slots are on the opposite end of the mobo (if you look at the quasi-BTX cases that use ATX mobos, the slots are at the top of the board when installed, BTX mobos move them to the other end, so they're once again on the bottom).
Power connections are also relocated to the top edge of the board, rather than a middle-ish location like most current ATX boards.
It's not just a case of turning an ATX mobo upside down and calling it BTX, it's a complete layout redesign.