I wanted to swap my Windows and Alt keys, so my keyboard shortcuts are more like macOS, since I have to work on both systems now.
I went into Keyboard Manager and mapped left Alt key to left Windows key, and left Windows key to left Alt key. Now pressing my (physical) Alt + R does NOT bring up the Run dialog. Neither does pressing my (physical) Win +r.
Pressing Alt (remapped to Win) + R brings up the Run dialog.
The screen just sort of blinks.
But nothing happens.
_Are there any useful screenshots? WinKey+Shift+S and then just paste them directly into the form_
I tried re-launching Power Toys as administrator. I noticed that with Keyboard Manager enabled, and my mapping in place, when I press (physical) left Alt + R, it pops up an error message.

Actually, it pops up the above error message when I press (physical) Win + R, too! Same error message pops up with both Alt + R and Win + R.
@arjunbalgovind this is weird, about half the keys seem to work. Win+E, Win+D does but Win+L does not nor does Win+R

This is related to #3188 and #2313. The Xbox Game Bar app detects shortcuts at a lower level than keyboard hooks. So if a user hits Alt+R or Win+R, since Game bar is at a lower level at some point it sees Win+Alt+R (the shortcut for recording). And Alt+L would not result in Windows locking since Win+L can't be overridden for locking the system.
To workaround this we will have try a similar work around to the Caps Lock IME issue (#4123), but I'm not certain it will work unless we test it with enough cases.