Boy, am I glad you didn't build any of our three homes!
Not one of the three contractors we used (one small, two mid-size, none of them big national chains) charged us for any changes that did not involve upgrades. ALL we paid for above the base price of the home was if materials and/or time would increase the cost to the builder. We moved walls, windows, adjusted opening sizes between rooms...not one cost us extra. We did upgrade an appliance here or faucets there, so those were extra out-of-pocket costs.