I have only about 6 or 7 inches between the windows, the common area of the two amounts to only about 9 inches tall and 6 wide (TC window high and offset to passenger side). I made a boot out of two layers of 4" foam. Just for the cat. On the previous TC it was a bit further, I made part of the tunnel out of plywood and hard mounted that to the camper. The flexible part only needs to be 4" or so to accommodate movement. The tunnel had a flange on the truck end so that foam could seal between the flange and the fixed part of the truck window. The tunnel itself had a bit of slope and offset in it to match up the misalignment of the TC window. I wanted to be able to close either window at any time to keep the cat here or there, so I kept the foam off the moving parts of the windows.
If you are worried about the paint, find someone who installs the 3M invisible rock shield "car bra" type of material. This can be had in sheets, is removable in the future without damage, and very tough. Have it placed anywhere you think will get touched. It is stuck to the paint with an adhesive, and won't allow grit or dirt between - which is what does the damage. It can be stretched around curves and cut tightly against window gaskets, clearance lights, etc.