I don't think you'll damage the roof, but be sure to strap the paddleboards better than you think they need to be strapped. I lost a paddleboard that was strapped to the roof of my Grandby when I experienced fierce side winds driving over the Antioch bridge in the California delta. Even though there aren't good places to attach the straps, I thought I had it well strapped. I didn't.
I'd be more concerned with securing them to a flat surface more than anything else. You always want to have the board deck down, mainly due to the fact that your wax will melt and you won't look like a kook . But with SUP's you probably just have the traction stuff on the deck?
I like the idea of using some pipe insulation underneath to keep them from getting damaged. Use some ratchet straps and you'll be OK. Not the most eloquent solution, but it should work.