I recently had a hole about the siZe a bit larger than a quarter. I used Dicor self levelling and it worked great. The next time I was at the dealer I asked them for a dealer decal to place over the repair. Lol!
2013 Jayco Sport
I personally hated the idea of making holes in my roof so I made a rack that allowed my canoe to rest on racks off of the front and rear frame.
Your Kayak may not be long enough to do this but just to give another idea