I know several people who had the builder carpet installed then ripped it out the day after closing and hired someone to install tile or wood floors. They probably saved 50%-70%. Honestly the prices they charge for upgrades are outrageous!!!! It is a bit more of a pain but it will save you thousands of dollars to do it this way. This is their prime way of making profits so they are unwilling to negotiate.
You can negotiate some sweet deals with contractors these days. I have a friend in University City who just dry walled and finished the garage, added an attic, laundry room, installed new interior doors through out, closet organizers in all closets, and new flooring in the hall and master bedroom for around $10,000-$15,000. The previous quote last year was $20,000-$30,000 and that was just for finishing the garage.