Palmy, a lot would depend upon what command the application
is sending to the operating system, I say that because some apps already have a key redirect for that and some other keys built in, so the OS redirect doesn't happen until it hits the OS. Hell, it may even be the app with the built in redirect is redirecting AFTER the OS, it's hard to say without opening up the code for each app and seeing how they're doing it.
Any app can be written to redirect any key or command, it's all a matter of what you want to do and take the trouble to do. The keys you mention are just function keys you can assign tasks to in the app, it's just they've been assigned certain tasks in the BIOS or OS in the past and are now assigned differently - the same way the old three fingered salute works different in Windows now.
I know of apps that will ALWAYS show evey damn letter key as upper case, no matter how you type it in the first place as the app redirects all character key commands to convert to the lower case ones.