About the cap? I keep my cap on the back of my pick-up all the time. It's VERY heavy, since it has built in shelves (2 shelves, each side) the entire length of the shell. Also, in addition to the spongie weather proofing seal under the cap and between the bed rails, I also caulked the gaps with silicon calking. Plus, it's wired for the stop like, and a dome light. To remove this beast takes a lot of effort and a total of 3 people, (to do it without damaging anything), it's just too heavy. So, unless there is an absolute reason for removing the shell, it never comes off. (Thus another reason why I never opted for a 5er).
I have a feeling, if you flip to a 5er from a TT, you'll not be using the cap at all. Better start getting your mind adjusted to not using it now, and save yourself your mind from agonizing over it later. If you can't handle the cap by yourself, you'll never put it back on.