Is it builder financed, or bank?

Usually, with a bank mortgage after a build, you will only be given a mortgage for what your house is worth, not what you paid. Often, that is less than what you paid, and so you will be "paying cash for them". But, it depends on your area, your appraisal, and your financer.

Do you have a construction to perm loan? If so, the loan is in process, as is the agreed upon price. Any upgrades will be paid by you. The only way to add them back into the loan amount is to do a refinance, which is cost prohibitive to do for only a few thousand dollars of upgrades.