In general, emacs is not interacting with the hardware at the level you're talking about -- if it were, then emacs would have to (re-)implement things like compose-keys that definitely belong at the system level. For emacs, as I understand it, each window system or terminal maps the specific interface to emacs' typical interface. By way of example, look at pgtk_gtk_to_emacs_modifiers in pgtkterm.c, which is pretty simple because the GTK interface is built on the GDK interface which grew more or less directly out of the X11 interface, which also birthed emacs' internal interface _for gui code_, but is not the same thing that emacs gets from terminal interfaces. This last bit is why, for example, Control-I, Control-[, and Control-Shift-Z are "tricky" for console emacs.
Another way to put it: despite the rumors/memes/stories, emacs isn't actually an operating system (although it's not impossible to think of it as a restricted virtual OS layered above the actual OS). It's probably possible to change emacs to make it closer to the low-level interface for a specific combination of UI and OS, and it would almost certainly break some abstractions for other combinations.
I hope this helps,
~Chad