I think this conversation is kind of orthogonal to the actual issue, which is that setting up the hardware to shift 32 signals from 3.3v to 5v is pretty easy. I definitely wouldn't consider it a "major pain." Interfacing parts which use two different logic levels is incredibly common, and there are many inexpensive ICs that provide bidirectional level shifting.

That being said, I think choosing a microcontroller which uses the logic level you need is a perfectly acceptable solution. Minimizing the number of components goes a long way towards making a project easier to manage.