Just in case I have the right idea, the following answer is provided.
A boot connecting the rear sliding window of the pickup to comparable front window of the camper is especially good with a pet. I took my 80 year old mother all over the west in our camper and she was very happy throughout the entire trip because her cat could come up to see her as we drove. The cat would lie on Mother’s lap, travel back and forth to the camper, where a litter box was set up and where it had another place to sleep. The boot made it so Mother knew where her was cat at all times, which is very important to a little old lady with a car. The boot added something to the trip that made it special and memorable for Mother and me. Ours was a canvas tube with hoops.
Mother had never been west of the Mississippi and I took her to see many of the great sites of the west, Grand Canyon, Big Sir, Muley Point, Mt. Rushmore, and many others. Mother’s cat would be up in the camper watching the world go by and waiting for us to return from our human ventures, restaurants, walks, and talks with people along the way. The boot was extremely important on the trip of a lifetime due to Mother’s great attachment to her cat.
Another function of a boot is the ability to go forward and depart from a camp without going outside. This adds security. A boot allows constant access to the camper from the truck while under way for driver’s sandwiches and soft drinks. It allows travelers to gain a little distance from each other. There are almost too many advantages to name.
Now the negatives;
We do not use a boot at present because they are less useful with our popup camper than with our previous hard sided slide in. It is not so convenient to crawl through the boot and get in bed with a popup camper. With a hard sided camper, the beds are convenient to crawl into at all times, the advantage being that a person can put on pajamas and go to bed for a long sleep while leaving others to drive. When the second driver/s gets tired, they can pull off into a rest stop and crawl in bed without disturbing the other person who has been sleeping for several hours already. Next morning, the rested driver can get back on the road early without disturbing the late night driver/s. A boot with a hard sided camper provides the advantages of a coach style RV. However, with a popup, the boot does not work quite so well in these respects.
Boots can be noisy. They cause problems with the heating and air conditioning. They can let dust into both the truck and camper. They can create a vacuum inside the camper which increases leaks when driving in the rain.
All these problems have solutions which involve making the camper a more permanent attachment to the truck. When the camper becomes too well integrated into the truck, the truck looses its versatility as an all purpose utility vehicle.
Damage to the paint is secondary to all these problems above. Probably the easiest solution to scuffed paint is to repaint the damaged area when finished with the camper. Of course, I know how to paint and have the equipment to do it, so I think it is cheaper and better to repaint the damaged areas than to worry with clear tape, etc.
With a small popup like an ATC or FWC, I think most people will decide a boot has more negatives than positives. Thus, the best solution to a boot with a popup, is to forget about it.
