If Keyboard Maestro sends any events, it will have the modifiers set as configured in the action.
I think what that means is that the modifiers are set "if KM sends any events" not "if you press the mouse." In other words, the action to press a modifier effects only keystrokes and mouse clicks that are generated by KM, not by you.
There's a chance I'm wrong about this, but that's how I read the post above. Perhaps I can be corrected by one of the real experts here.