No way it flies upside down. That’s not supposed to be done over politics in my opinion.
You are absolutely correct. The upside-down display of the flag is to signal actual, immediate danger (the visual equivalent of a 911 call), not political butt-hurt.
As for displaying any other flag above the U.S. flag, that is a direct insult to the nation. Better not to fly the flag at all if you can’t display it properly.
I can’t believe how many FR posters think it’s somehow OK to disrespect the flag if they can convince themselves that their disrespect is somehow motivated by their notion of patriotism. That logic escapes me.