What kind of problem would require removal of floors? I can only imagine something structural, and you should be able to isolate that (low spots, creaking/movement, etc) before you go and spend a few grand on new floors. Can you opt for the builder not to install flooring at all?
I know when my brother bought his house they had to come back to about half of them and put more NAILS in the floor to stop the squeaking. I asked him why didn't they use screws and he said he offered to buy the screws himself but they wouldn't do it, nor would they allow him to do it himself.
They charged him 800$ to install a 300$ Moen facuet.