Question: I'm guessing your in the Southern Hemisphere. Are you running a double deep 8 frame like most of us Northern hemisphere folks are ?! Sounds like your chilly Wx would have been a wise candidate if not.
If you are going to have to leave the Flow-Super on for food storage I'd remove the Q.E. forsure so your queen doesn't get left on the wrong side of the excluder fence !
A pix or two would be helpful telling you much n your minimum profile is not very helpful n giving your location or other valuable info to accurately give you the best help.
Good luck bro. Watch your Girls Careful this winter so the have enough to survive.
P.S. I personally wouldn't n dont leave my honey extra honey supers or Flow-supers on. But not sure you have an option this late in your autumn down there with the dip in temps now.