PCB space is not a problem, I'm going with an atmega 32u4 directly on the board (in the area between enter ctrl and fn on the backside). Using these daughterboard things just seem like a waste if you're going through the trouble of designing a pcb anyway, and one surface mount component is manageable. USB is onboard, and comes out above the Alt key.
For the most part, since I added in enough keys to cover my applications, including the numbers, I'm not going to be using the Fn key for anything except the F keys and brackets, I don't use those much. Also, the location of Fn and Alt are both fairly close to the index finger position, I never liked using my little finger for those anyway. I'll give it a try and if its a bust, it can be easily reprogrammed.
Worst case scenario, Fn gets moved to the "? /" position, though I really like the idea of having only 1 set of mods which are accessible by both hands.
The higher thumb keys are really made for the index finger, you rarely use space and ctrl, or enter and backspace at the same time, it shouldn't be a problem.
The only real issue I foresee is that I may find the home row to be too low for my comfort, and swap the number row down to the bottom to shift the home row to the middle of the keyboard.
This is pretty much a modified version of what I use on my ergodox: