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Glue?
Hahaha - totally joking. What about some sort of mount that is held in place when you shut the back tail gate or one of the side doors (similar to the sports team flags that people put on their doors/windows of their cars).
Are you willing to drill? The rear bumper cover would be a good spot since you don't have to worry about rust, etc.
-Rich
I've seen a couple of roof racks that work on suction cups - they claim to hold up to 80lbs at highway speeds - I'm sure this sort of tech would do the trick, assuming that the flag pole itself is relatively flexible (thus relieveing some of the movement stresses).
The suction cup stuck on the boat glass has never failed, even at 25 mph. If this bothers you though, you might try the clamp on style boat flag and clamp it to your roof rack. What is the rule for your flag? You mentioned it must be six feet long. Is that measured from the highest point of the vehicle or from somewhere else?