Rooftop transport

Your dilema is really only going to be when it is cold out (like winter), and not as big of an issue in the spring/summer months, correct?

So, my suggestion would be to add the appropriate racks to your truck, AND install a battery blanket for the truck battery, as well as maybe a small space heater for the cab to keep it above freezing temps. Then just park it outside and all is good.

Problem solved!   

I once had to tie a kayak to the top of a rental car with just a couple moving blankets between the car and kayak. My truck died on the way to a redfish tournament with 300 miles to go and my rack wouldn't work with the rental. Straps forward and aft to the corners of the bumpers with some tension and one to keep the blankets around the kayak worked. I had to  make sure the straps can't slip where they meet the kayak and go a little slow around corners. I imagine anti-fatigue mats would be better with that same application because they won't slip but they are also more expensive. You will also likely scratch the top of your canopy a little and may rub the paint where the straps come down, and yes, the rental had a dent in the roof where the kayak was, but they didn't charge me for it because I returned it at night