OCR,
I built several homes, and here are my suggestions:
a. if the standard counter top is granite, then you should try to pick their no charge granite. However, usually , the no charge granite is not very good color wise. I found it is very expensive to upgrade granite from their standard ones to a color i like. I actually would suggest you get quotes from a reputable contractor before making a decision to go with the builder or not. As long as you use a reputable contractor, you should have no problems doing it after the close of escrow. Pacific Sales has very good contractors. ( I don't work for pacific sales).
b. For epoxy, i won't do with the builders. Remember, again, builders don't do anything. They SUBCONTRACT. So, again the trick is to find a reputable contractor to do it. Just walk around the neighbourhood, and find a referral.
c. You do need to consider doing some electrical work with the builder, because it is difficult to add later. For example, adding recess can lights for the first story of a two story home is very difficult. if you have a ele dryer, and they don't have the 220v connection, then you need to ask them to add it.
d. flooring? well, i won't do it with them unless you have left over credit allowance.
Finally, remember, for every penny of upgrade with the builder, you will be paying property tax for as long as you live there. If you do yourself after escrow, you will never pay property tax on those upgrades.