Is there some way to offer this product without the voltage divider on the headers? Or updated product with just pmod connectors? The major issue is interfacing to the header with devices with 3.3v
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.
Why don’t you just remove the pull down resistors (R153, R155, R157, …) that form the voltage dividers?