Hi, Douglas. Very good on you to be paying such close attention to one of the most misunderstood (and important!) docs regarding closing. The closing statement is used only going to determine how the terms of the actual loan are to be paid....if the builder was offering closing cost assistance, it would show up on the statement.
If you have previously negotiated free upgrades, this should be part of the original contract and enforceable. The price of the home that is listed on the top of the HUD/Settlement statement (line item 101) will reflect the price of the home. Make sure it is the price negotiated on Contract and you are set!
Best to you and ALWAYS get a home inspection before you close!