After doing some more reading and figuring, I have a conclusion.
Yes, it is better for the boat to carry it upside down. It also better for the boat to support the hull with long runners rather than 4 tiny spots (crossbars, etc.)
The plastic that hulls are made from is pliable - which is good and bad. Good, because when you hit a rock in the river, the hull will flex instead of crack.
Being pliable means the hull can change shape when forced. Such as, when you crank down on the straps holding the boat on your truck. To prevent unwanted shape changing, the hull needs to be supported to spread the load over a larger area. Which is why long runners are preferred over bare crossbars or similar carriers.
In use (on the water), the entire bottom of the boat carries the load. Large surface area, low load per square inch. On a rack, the load is carried by only a small area of the hull. High load per square inch. Load gear in the boat, and the load is increased even more.
So, right side up or up side down, more surface area of the carrier is good for boat life longevity.
That being said, the shoulder of the boat (intersection of side of hull and deck) is probably the strongest area on the boat. The raised rail around the cockpit, not so much.
I built a cradle to carry my boats upside down. Unfortunately, I had to build a second cradle when I got the second boat. The boats are different enough that one cradle does not fit both boats. And, you really need 2 people to get the boat on and off the truck. But, taking it on the road for 5 hours to ARV, I don't worry about anything happening to it.
Here is a photo of the cradle I built for my new, smaller boat.
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The runners are 2x4s, with 1x2s sitting in rabbits along each side (the raised lip.) The inside is curved, matching the boat. The aluminum strips just maintain the spacing - they don't carry any load.
Here, you see the cradle sitting on the boat.
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The cradle attaches to a set of Yakima bars, which attach to the truck.
Here is shot of the cradle for the tandem, attached to the Yakima bars.
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I've been rambling - I hope this makes sense. If not, just ask.