If you are just want to use standard mods on the foot pedals it shouldn't need to be made to function with the keyboard itself. When I hit shift on my orbweaver, standard keyboard (yet to test with PS2 connected keyboard) or one of the side buttons on my Naga, it seems to function global. I can hit shift on the Orbweaver and my Das will type capitals. Since ctrl and alt are actual key codes being sent to the PC as well as shift, to my knowledge at least, it should work. Though function layers are completely field in the keyboards firmware, so that would have to interact with the keyboard itself.
Please take this with a grain of salt but this seems to me how it would work out.