I'd actually raise them off the floor if you can, even by a couple of inches.
Mold underneath the polystyrene would depend on what the humidity is like down there- if the window is badly sealed or it's old, you might have an issue. Best thing to do is try!

I have a house that gets VERY cold in the winter; I ended up blocking the windows in the snake room with the plastic insulator shrinkwrap stuff, with blankets over that. I also (and I think this was more helpful) used foil covered foam insulation on the outside walls of the cages that weren't up against any other cages. This actually really did wonders for heat retention. Not the prettiest solution, but saved us a LOT of futile heating.

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