I did talk to a GC friend in another state and he pointed out a few things I wasn't considering, but still...
The builder is factoring in tear out and haul away of existing carpet and padding, the trim work with the baseboards and any leveling that would need to be done. My guess is they get all of this quoted out and maybe it's around 3k and then they double it as a mark up.
I have inquired about if they have already placed the order for my flooring selections. If not I'm going to ask about removing the flooring from the contract altogether but I am not optimistic that they will be amenable to this, and even if they are I can guarantee you the credits issued will not come close to adding up on a sq ft basis to what he quoted for the additional flooring.
This happened with the painting too. Painting was our responsibility, not part of the contract. When the drywall was done, both the builder and I thought it was a good idea to paint before the cabinets started going up in the kitchen. I asked him to send his painter out for a quote. Large kitchen plus office basement plus dormer addition/master suite and he quoted me 13k for priming and painting. I laughed in their faces. I had a crew of Mexican guys come out the next day and did the entire job for $4k.