Actually, you shifted what I wanted to say where a bit: I meant that while the current FPGA can do 3.3V, I am not sure how many others can do so.
Ah, sorry. Well, Cyclone IV and earlier can, as can Spartan-6 obviously. Kintex-7 and Cyclone V will apparently also support 3.3V IO on at least some pins, though I'm not sure if they do for the configuration pins...
I don't think there is much reason to discuss other FPGAs here. This board will have the Spartan-6. If someone wants to make a board with a different FPGA later, nothing is stopping them from using a different MCU or different method of interfacing with the bus entirely. The daughterboard is self contained, it just needs to conform to the specifications of the DIMM connector and bus interface, so that it's compatible with the motherboard.