> Just swapping the key caps is not enough. The keyboard also has to swap the scan codes it sends, since the code for Alt is the same as the code for ⌥, and the code for ⌘ is the same as the code for ⊞.

Alt and ⌥ are on the same location on the keyboard, likewise ⌘ and ⊞ are on the same location on the keyboard. So it seems that just swapping key caps should be enough to get proper support.