Different kitchens can change all kinds of costs, adding frame work for granite counter tops for example or bigger rafters for same roof line but slate or concrete shingles. A 2000 sq ft home's price can litteraly be doubled in just having different finishes. Porcelain over ceramic tile, heated garage vs. un-heated.
I have been in the industry for 20+years and home building has a small margin and big headaches, namely weather, un-decided change orders and prima donna tradesman. Some hard learned, free advice is, when you are prepared for the worst and face it with determination, than it generally goes better than having everyone under the gun to finish on a schedule. Better to have a well built home that does not squeak, lights all work and you received all the bells and whistles that you may want than have one that is done in 6 months but the can lights shine through the ceiling fan creating that highly sought after strobe effect or your garage door shuts but there a 1" gap under one side that snow blows in creates a great drift in your garage that is supposed to be heated but is not etc, etc....
Just know your blueprints and treat your tradesmen with respect. I have seen more Architects be wrong than carpenters when having....let's say heated conversations about interpretations of the blueprint. A good Architect will listen to the tradesman. Good Luck!!!!!
I know that you have a Contract that covers your butt for Contingencies and Extensions.
I know you have a Realtor representing you and protecting you.
So, what's your problem?