The reality is, once you have committed to a builder, there is zero incentive for them to provide a competitive price on anything going forward from that point. (An unscrupulous builder could really take advantage of this.)
In order for you to get the best possible price, you need to decide on as MUCH as possible, ahead of time.
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This includes 'allowances'. An allowance is a monetary-figure (often arbitrary) that is included within a construction contract, for something that is necessary, but is initially undecided.
Windows and doors are a common example of an allowance; however it is not unheard of to have dozens of allowances in a contract.
With an allowance you ultimately will be pay the actual cost, when that is later determined. Problem is, at the point, again there is ZERO incentive for the builder to provide a competitive price.
It is really in your interest to decide as many things as possible prior to getting quotes. It might seem like a lot of work, but you have to ultimately make those decisions anyway; just make them earlier, and save your money.