Emulators will always need to get modified keymappings compared to the PC version, because no sane emulator author would map the game action buttons to Home/End/PgUp/PgDn by default. So I don't think it's a huge problem to also remap the F-keys to something more convenient.Emulators? IIRC mednafen on PC uses F keys to enter configuration modes. Of course anyone who ports an emulator can change that, but with the Pyra being more able to run more powerful emulators without so much optimisation, it will mean that some emulator ports require more work than they otherwise could do.Now, as far as I know, the number of game devices that actually have both F-keys and shoulder buttons is zero. PC-games may use F-keys, console games may use shoulder buttons, but I don't think there is any type of game that originally uses both the F-keys and the shoulder buttons.
Perhaps emulator authors could do something simple so they keyboard sticks in Fn-lock mode so that you can use the number row without having to go through the code and modify every keyboard event code. Or we could go with Kingu's soltution with an F-button key (I disfavour the word 'F-ing' by the way).
The point of having useful stuff (like modifiers) on the shoulder buttons is that it's useful; obviously that means that if you're using the shoulder buttons as actual shoulder buttons (like in a game where that makes sense, in particular on emulators that emulate systems which had double shoulder buttons), then you'll have to sacrifice some of that usefulness. We could of course also map the shoulder buttons to numpad 1234, ensuring that there are no clashes whatsoever, but then you lose the convenience of having useful stuff on the shoulder buttons.
The F-keys are mostly used for DOSBox/QEmu stuff, as well as many desktop applications. Luckily, that software expect a normal keyboard (and mouse), not a game controller with shoulder buttons. So it makes perfect sense to have the modifier that is needed to produce F-keys available as a shoulder button.