Well, SEA is the arduino shield.
And the vast majority of arduinos out there is 5v, so …
If you need PMOD and 3.3v vccio - SEA isn’t the product you should be choosing 
There’s still room for 3.3v io. Fpga io’s 0 to 9 is connected directly, so can act as inputs, or host one 8-line PMOD.
Arduino io’s D2-D13 won’t divide the voltage when acting as outputs, but 1k resistor combined with connection capacitance will drop the max data rate on those pins.