I don't have any idea what the boot was that was on the Stockland camper shell that came on my 84 Ranger pickup but it didn't rub the paint off the cab of the truck. Not sure who started spreading that around, but if its installed properly you won't have any paint rubbing issues, the boot is designed to be able to move and flex, if it doesn't don't get that particular style of boot. The one that was on my ranger was extremely flexible, and was permanently glued to the camper shell, the shell itself didn't have a front window in it, so you just simply closed the back window of the truck cab. Had carpet in the Ranger and it really helped with road noise. I'd rhino line or linex the truck bed, that will help with noise too.
When I got the shell for my tundra the dealer had no clue what I was talking about when I mentioned a boot, so it wasn't until later on I found if I would have ordered a Leer or an ARE I could have got a boot. Get the accordian style if you can, they have the most flex to them. If you drive on rough roads you want the boot to flex as much as possible. The biggest issue I've ran into with the tundra is trying to seal the shell to the bed so it doesn't leak. The front of the bed is really narrow, so you need quite a bit of weather stripping to get it sealed properly.
How often are you going to remove the camper shell? If its something that will only be used once or twice a year use clamps. If you want it permanent, bolt it down. The clamps didn't stay on very long with my shell on my tundra, I threw those things away pretty quick. Use 6 bolts, 2 towards the front, 2 towards the back, and 2 in the middle. Use bolts with locking washers and/or self locking nuts otherwise you'll forever be crawling back there to tighten them down.
Get the windors in the sides of the shell, they're extremely useful. Also, get a high back shell rather than the cab high model...I can't count the number of times I either hit my back or head on the back of the shell trying to get in or out of it.
My truck sat level after the shell was installed, but it was pretty much level prior so I didn't notice any difference, but my truck bed was also heavily rhinolined as well so that added a bit of weight too.
Get the 12V LED light package, don't let them install the cheap ass battery powered lights that they love to push. I didn't realize how much I used that dome light in the camper shell until I went to use it and the batteries were dead. So the past 2 years I had the truck I didn't have a dome light in the camper shell. Never bothered taking it apart to replace the batteries as I had wanted to replace it with the LED light package but never got around to doing so.
Go with rhino lining or linex bed liner, and get the camper shell with the carpeted sides and roof, it really cuts down on noise and I think will keep it a bit cooler back there as well as it kind of acts as an insulation as well.