cscape is of course 100% right, but hey, I work on these things late at night after the kids are asleep... so level shifters: if one is good, then two must be better. Also, you could make an argument that when driving board-to-board 3.3V has a better noise margin than 1.8V.
That was my plan with the CPLD - 1.8v I/O within each board, 3.3v between them and the controller board.
Unfortunately I didn't think through the implications of powering the rpi independently of the 3.3v to the board during bring up - I wanted to be able to measure the board's 3.3v draw. Unfortunately if you power the rpi up before the board, you send 3.3v into an unpowered I/O pin on the CPLD and the chip goes into latchup

I would have liked to have c-scape in my design review to say 'you don't want to do it like that!'