If you follow that argument to it's conclusion, all pop-up menus are entirely flawed since a user might try to click somewhere within the menu before it's appeared. So the Start menu already needs to be ditched because it obviously doesn't work. Moving the mouse into the corner and clicking is the only thing that could be relied on.
I think the reality is somewhat different, especially given the Start Screen pop-up is considerably less complex to draw than the Start Menu (it's a static image after all). Although it wouldn't exactly be difficult for Windows to treat clicks as if on the pop-up UI if, for some reason, the drawing is suddenly delayed.