I stack all my AP cages flush with each other and use flexwatt for all of them. It's fine. Now if you are using a RHP on 1 cage, I would put that cage as the top cage. Putting a cage using flexwatt on top of the cage with a RHP is going to give the cage above the RHP false readings whenever the RHP comes on as it will warm the floor of the cage above it.
And if you really want, you can shim the cages using something like furniture pucks. Can find them at pretty much any furniture store. Just non skid little plastic pads.