deacm,
1- That is the recommended way to carry the AI. You just have to make sure you have enough clearance between the rack and the vehicle so the aka crossbars don't scratch the roof. It usually means you have to flip the AI once up as it's easier to slide the hull right way up first.
2-Pirates pillows are not necessary when the hull is transported inverted. They were made out of insulation foam designed for pipes and doubled over where needed to roughly match the profile of the hull when transported right way up.
Don't the Thule bars have some sort of rubber insert to stop the load sliding? That's all you would need.
BTW- You don't need to go too tight with straps. Ratchet straps are overkill and could dent the hull. Cam lock straps are fine. It's also a good idea to secure the bow and stern with a line.
If you do transport the hull inverted remember to jam some pool noodle into the mast receiver just in case the balls come loose.