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My question is, will the floor eventually "settle into" the uneven spots, in effect taking the shape of the wood floor underneath as the floors are walked on?
No, not in a floating installation. If there are any uneven spots in the subfloor, you will always have movement. The bigger question is, how much movement is there? If it is very slight, and the subfloor was checked for flatness and was within Bruce's tolerance requirements, you shouldn't have any problems. If the subfloor was outside of their specifications and you're getting a good amount of downward deflection, you're likely to experience some creaking/squeaking as the boards rub against one another, and with that product (Lock and Fold, I assume?) you could actually see the end joints separate over time.