I recall having a conversation with Brian our builder recently about how most contractors make their money on changeorders. It's the dirty secret of the business and it's something you should definitely be aware of. We got into the conversation just as another potential customer was asking why Brian's quote was higher.
In bidding for a job, an unscrupulous contractor might specify a low grade of lumber, low quality windows, cheap carpet, low allowances for finishings and a whole myriad of tricks. As an unsuspecting home owner, you just don't know what you are getting in the quote because it is very hard to spec everything out in advance as you would want it and then compare apples to apples on quotes. Then you sign the contract and you are totally stuck. Everytime you are disatisfied with the material spec in the quote, its "changeorder time" and you can get totally raked over the coals on price with no choice now. Beware!
Fortunately, our builder Structural FX doesn't operate this way and we have not had to experience that. The changeorders we've had have been extremely well handled with very reasonable price changes - often none at all or simply materials, not labor, even on some significant items like additional foundation height and walls! That's what we really like about them, they are totally honest and willing to work with you to make the best of any issues that come up.
It's something you should ask the references for your contractor about - how they handle changeorders - and try if possible to get someone who knows about building to help you ask the right questions on the quote they provide - what kind of lumber, where from (call the lumberyard to ask if this is their best quality or what the tradeoffs are), windows, doors, roof type, electrical finishings, plumbing materials etc etc. Do your homework here and it will pay off big time.