I will define a list of keys: LeftShit, RightShift, LeftControl, etc.
The platform dependent code will decide which one was pressed. As events
will be invisible, I don't think we will interfere with input methods.
I caution you to think about this very well, there are *very* many
non-standard keyboards or remapped keyboards out there, where users
expect everything to work.
In general, it is best to leave the mapping of physical keys to intended
keypresses to whatever the operating system provides. In the specific
case of Xorg, please only look at the keysyms, do not try to do anything
magical with the scancodes, this will only result in a broken
implementation.
I understand the wish to have this, but it is a way more complex topic
than it looks like from a first glance.
I have had to deal with way too many bad implementations of this than
wanting to deal with it in Emacs as well :-/
Sorry for the criticism, in case you have already thought about all of
this and solved it, I'd really be interested in hearing more about it!