It will have up to 4 PLLs, so you will have a lot of options for clocks. The 16MHz clock source is not set in stone, I have some flexibility in the clock frequency I pick. The prototype boards I ordered for manufacture will have 16MHz clocks on them.
I think I would have to change the board too much in order to support 1.8v GPIOs. I’ll take a look at it, but no promises. I already ordered prototypes and they were so darn expensive.
On the other hand…this isn’t the last board I’ll be making with the ECP5 FPGA. I’m planning a larger board that may have programmable voltage regulators for the IO banks. This would let you change GPIO voltages dynamically. That future board will be something like 4" x 4".