Ah, yea that would be a deal breaker for me if I wasn't able to get the kitchen I wanted... yes, you could replace stuff later, but out of your own pocket for something you should have been able to customize when you bought the house. I'm not you of course, but you do need to weigh how annoyed you will be with compromising on things. My only regret in our home purchase was that I wanted the iron staircase going upstairs but I found out after we had already ratified our contract and doing our design center stuff that we could not get the iron railing if I didn't have hardwood going up the staircase... and if I wanted to change it I would have to pay a fee to change the contract etc etc... so, now everytime I look at the stairs I am just slightly annoyed cause I'm looking at white wood. Can I change it? Maybe later... but it will be a long time before that is on my priority list to change.
You don't want to make a big investment and then end up regretting things later on. So, as long as your comfortable with it...that's of course fine. But, just make sure its the right thing to do for you. 
There are no other builders or neighborhoods worth looking at to at least compare? Personally, I would at least check around a bit to make sure that there was not a better deal to get all the things you wouldn't be getting with the builder you're with now.