I’m pretty sure you could do that too, with a little coding. (Meaning, both function keys normally act like ShiftToLayer(FUNCTION), but when both pressed, it does ShiftToLayer(FOO) for some other FOO.)
If you’re comfortable with coding, here’s approximately how I’d do it. You’d start by making both Fn keys instances of a macro. When pressed, you check if the other one is currently pressed (maybe there’s a static flag in the macro function), and if it is, return MACRO(Tr(LockLayer(FOO))), but if it isn’t, return MACRO(Tr(LockLayer(FUNCTION))). Then on release, unlock the layers as appropriate.