21st Amendment started their watermelon wheat by processing whole watermelons at the brewery.Since they had a local juice processor deliver watermelon juice.
I'd use 21 Amendment's Watermelon beer as the exemplar of how to use watermelon in a beer. Watermelon is a very delicate flavor and artificial watermelon flavor just doesn't taste right. Given the limitations of the flavoring, 21st Amendment gets it just about perfect.
Personally, I'd puree watermelon meat (and some of the inner rind) and add it to primary late in fermentation or in secondary. As long as the watermelon isn't cracked the pulp itself will be sterile/sanitized. And, if you use sanitized tools (knife, cutting board, bowl, blender/juicer) there's no reason to pasteurize the juice.
The only way that I could imagine concentrating watermelon puree is by freeze or vacuum concentration. Boiling would just caramelize the sugars and drive off the delicate flavor and aroma compounds. You'd basically end up with sugar syrup.
I agree that some of the flavor of watermelon is actually rind, or maybe that's just residual watermelon flavor after the sugars are fermented out. If you're using whole watermelon, I could see using underripe melons or making sure that you get a fair bit of the inner rind with the meat.