Got it.

W/o a seal, you'll probably always have to deal with this problem. I never noticed it on my 99 tacoma, but I don't think we had a lot of snow that year.

 

I feel the need to make a really stupid suggestion so here it is:
http://new.custom-magnets.com/produc...339&cPath=2_47
Wax the bejesus out of the shell so it has a thick sacrificial surface to prevent abrasion from dirt particles that get underneath it. Buy a few feet of this and slap it on top of the cab with most covering the cab for a stronger grab on the magnet. Voila! Gap covering, no holes drilled, and instantly removeable. They use this stuff for automotive signs so it should be up to the wind forces that might otherwise pull it off.
Heck, you might even be able to get it color matched.
There, I've done my bit for advancing the potentially feasible, but equally likely absurd for the day...

 

My dad uses a bike inner tube between the cab and canopy. He sticks it in and pumps it up, seals pretty well.
He camps in the truck alot so he just leaves the sliders open and heats up the canopy that way as well. Worth a try, it's cheap and doesn't rub on any paint.

 

On my last ski trip I had a build up of ice between the cab and cap that punched a little hole in the cap as I was driving. So it can cause some damage. The snow was melting and refreezing forming an ice dam. I had to fill the hole with some silicone caulk. Sorry I don't have any solutions to offer except to get up there with a broom and sweep it off time it snows.

 

This option may be obsolete, but I've had the same problem. What about using a pool noodle, or piping insolation as mentioned above. Depending on the width, it would be a good snug fit, and being foam wouldn't cause any abrasions or scratches. I have not tested it yet.

I have seen the inflatable truck boot online. They run for about $30.00. I may give that a try.