We generally leave our Super High Wind PUG's in place.
I removed them on one trip this summer because we were having to pack up with the bunk ends a bit damp. Used a short step stool we carry to climb on the bunk end to re-install them. Only issue is to remove the Reflectix window panels prior to climbing up, as it is difficult to prevent crawling over and bending / crushing them.
With the shock cords gathered and hooked together with two carabiners it is pretty easy to prevent jamming in the door gasket or tangling the cords.
We do not leave our thick mattress toppers in place though. Thinking Reflectix, PUG's, and toppers all jammed in to the bunk end might be a bridge too far.