Nope...no trouble at all.
My CVT has a pair of aluminum rails that is mounts on, this is the stock way to fasten it to whatever it is you want to mount it to. You slide in the stainless hardware, and away you go. This raises the base of the RTT about 3/4 of an inch off the lid. Also with the way my sides slope down on an angle to match the tub, I have lots of room.
Can see in this pic how much space there is. The flap hangs down over the zipper an inch or so all the way around.