I know that "media keys" (e.g. a Calculator button) aren't actually keys but another kind of USB HID device hanging out on the keyboard like a Touchpoint mouse; but F1-F12 keys really are keys, events sent from the same device that sends regular keysyms. Are they just random non-positional codes hiding out outside the ISO 9995 reserved range?
Control/shortcut keys are bound to the physical key, not to the regional layout characters bound to them. The displayed shortcut is often shown as the one for the US/UK layout.
As someone that often switches from US layout for programming to local layout for a few national characters, I'd consider any other behavior to be incorrect.
(People using QWERTZ/AZERTY might not agree/don't switch layouts that much. I'd be really annoyed if location for Ctrl+Z moved around... This is why standard key for Undo on PC was Alt+Backspace, which I still often use).
There's no reason that would have to change. If the OS was aware of both the key's physical location and what character it was supposed to represent it could easily keep the same physical mapping while simultaneously displaying the correct characters for that mapping.