The 1000sqft house versus a 500sqft house probably only adds a half bath. Its not like you're going to jump from one bath to five in another 500sqft. The plumbing work on adding a half bath in new construction really isn't too much when properly planned.
Proper planning generally means those bathrooms are right next to each other, so the toilets use the same drain and vent pipes and water supply except for the last 2 feet. You ideally put the kitchen and laundry close as well. Of course you often cannot put everything close and that add cost, but it is attempted.
Don't larger houses have multiple bathrooms, thus not the same cost for plumbing? At least when I watched Selling sunset, it seemed it's about having at least 3-4 bedrooms and 4 bathrooms in a house...