Disregard that... I should have checked the Flash datasheet before posting, it doesn't look like it can be programmed via JTAG. I only remembered seing the word JTAG somewhere in the schematics. Now if the FPGA could be coaxed into a programmer via the JTAG port... Anyway, the point was that if possible, a standard programmer could be a good idea if you want to get the board out quickly and don't risk as much money.
I'm looking at the old "Bottom+Layer.pdf" and "Top+Layer.pdf" that was posted some time ago. Are those deprecated? Couldn't find "J2" in the schematics, but J4 looks like it is still in place. Only had a quick peek though.
If you go for options 1 or 2, will you use the same board, leave the expensive components like the ARM unsoldered, and fix the rest with the FPGA? Or will it be a different board?