Save the money now (a false economy). If you insist on the lowest cost per square foot when you build the house, you won’t get good quality anything. And, not many years down the road, you’ll be facing multiple replacement costs as the windows, roofing and other things begin to give out. You will also face higher utility bills every month you live there.
Save the money later (financially prudent). Pay more initially to get good quality windows, better roofing, solid framing, and upgraded insulation. Better quality for these basics saves money later because your maintenance and replacement costs will be far less and so will your energy bills.
The short time-frame fallacy. You may anticipate that you won’t own the house long enough to deal with replacement issues, but most people stay put for longer than they expect.
The builder’s mortgage. Do not sign onto this when you sign the sales contract unless your builder will state in writing that (1) the mortgage interest rate at closing will be the current prevailing market rate (otherwise he’s contractually free to charge a significantly higher rate) and (2) he will only charge those closing costs that are legally required.
Get it in writing. The builder’s sales agent can promise you the moon to make the sale. But the only promises that count are the ones that are written into your sales contract.