Just to be clear : I don't talk about layout preferences and needs for characters (I'm a partisan of making your own layout to suit your exact needs) but about the level under that, the keycodes input by the keyboard itself. If the keycodes are directly input without any additional software, it's best for compatibility and anybody can make a setxkbmap command to change the default qwerty to its favourite layout.
An hard coded Fn layer allows to input keycodes instead of a soft coded layers in an xkb file which be unacknowledged by the kernel. Us-qwerty is just the legacy layout of the Linux Kernel : The one he understands without xkb config file so IMHO it's important to keep it because of Magic Syst Req keys. This Fn layout can still be rearranged if the keyboard micro-controler is reprogrammable (or maybe by the Boot file used in ARM arch instead of BIOS, I don't know well the possibilities of this booting process) so there is no problem for customisations. I don't know what issues occur with Pandora's Fn key but if it's cleanly done, there will be none.
In addition to Syst Req keys, some (bad programmed) games use keycodes directly instead of characters input and the majority doesn't allows to configure mapping, there are still plenty of FOSS games in this case (and if one day Pyra provide an x86 CPU board, it will add the proprietary ones). Any game or program using keycodes without taking care about layout will correctly run as is without wrong layout issues and the us-qwerty labelling will match their prompted keybinding help. That's a very common problem for those who use a dvorak-based layout.
So, that's why I think the keyboard need an hard-coded Fn key independent of the OS and why the us-qwerty should be the default label on keyboard.
Concerning interchangeable keyboard clipped on the Pyra (like a mix between the Typematrix skins and spare keyboard part of a laptop) that's a pleasant idea but the actual design isn't made for that and all those optional pieces will increase the price. And they still will be people unsatisfied because one or another layout labelling isn't available (colemak, Neo, belgian azerty, swiss qwertz, korean, uk-qwerty, customised layouts, etc. )
To me, a better solution is relegendable keycaps as it exists for Cherry MX keyboards (used mostly on Point of sale keyboards like Tipro do) because it will please anybody, but again this might increase the final price.
