The builder should be at least as concerned as you are with a good appraisal. If your new home does not appraise, the lender may not give you the loan you need and the builder risks losing the sale. In addition to that, your home becomes the next best comparable for similar homes built in the neighborhood. As a result, if your home sells for less, it will affect the value for the next several homes built by the builder in your community.
The appraiser should be aware of the upgrades and appraise the home accordingly. In my experience, most appraisers look at the contract price and do their appraisal around that price. The fact is, you will get an appraisal showing your home is worth what you paid for it. It really is not a real concern right now as to how much over that the appraisal comes in at. Since the appraisal problems and sanctions of recent years, I rarely see an appraisal come in for much more than asking price. It will be interesting to see what value your home is appraised at with the incentives built in. You can let us know if you don't mind. We like to monitor those things.
Robert McGuire ASR
Your Castle Real Estate
Direct - 303-669-1246
If you are allowed to use your lender of choice here in Colorado I would be happy to prepare a quote for you. Just let me know.
Nothing is ever really free, usually the costs for upgrades are already built in. Builders do not like to lower their price, but will include more things instead... you should compare the builders lender's interest rate and costs with your own and choose the best one.