I have two ways to press F5: I can press Fn+5, or I can press 5 and the key below (Y on Dvorak) together. I usually use the latter, since it can be done one-handed, but I would still prefer a real key.
My next keyboard is likely to be something like a Dactyl Manuform, and I don't see the point of _not_ including the F-keys when I'm printing the case myself.
I don't miss dedicated PgUp/PgDown/Home/End keys. I have these as Fn+↑ etc, which is fine -- I mostly use these keys when I'm typing with both hands, whereas the F-keys are often useful in combination with the mouse.
I use chorded keystrokes for F-keys. I have a layer key (named “Lower”, and located where the ‘Windows’ key is on normal keyboards); hold that down with your left thumb and the middle row of keys on the left split (caps lock -> g, under a qwerty layout) become F1->F6. And the bottom row of keys on the left split (left shift->v) become F7->F12.
I actually find it a whole heap easier to hit those key combinations than trying to find various physical F-keys three rows away from the home row; I think I’d actually set up a macro like this even if I was using a full-sized keyboard; I just find it to be easier.
(although I don’t actually use F7->F12 for anything, normally; that might be a little awkward in terms of finger positioning and I’d think about maybe moving them over to the right side of the split if I used them with any regularity)
I agree that the usage of the F-Keys is a little bit complicated, especially if you have small fingers.