Your contractor will be able to tell you exactly what the plans include. In my experience with Habitat for Humanity the basic house that is $XXX.xx per foot has XX, XX, XX, and XX included in that amount. If YOU want OO, OO, and OO instead that is an extra charge.
We allowed the future home owners to pick from a couple of counter tops that were very close in cost, then the flooring had 3 different linoleum choices, a few different carpet fibers in various colors such a a Berber, short pile, etc..., and then the color theme in the whole house.
If they wanted hard wood floors they had to use their spending allotment for that. I think it was just a few thousand dollars that was a free bonus to them to be used where ever they wanted. We had one home future home owner who had a son who had Down's and he did a work program through his high school. He worked for a man who contracted flooring for home builders. He gave her all her flooring at cost and installed it himself. She got the most awesome carpet!
Another home owner had a friend who did cabinetry. He did custom kitchen cabinets for them at his cost. They were solid wood and totally beautiful.
There are many things a basic house has that a showy house doesn't have. Such as crown molding, tray ceilings, custom cabinetry, all sorts of lighting extras, you must get the contractor you choose to put this all in writing.
I have a friend who moved to Spring Texas and they had a house built just a couple of years ago and they paid something like $47 per square foot. I can't imagine it really being as high as your Realtor is saying so be sure you visit with every reputable contractor you have in your area.
There are going to be some that are newer to the area, maybe don't have a lot of reputation, etc...but may be really good builders. They may be looking to get a foothold in the area, go visit some of each contractors homes and decide based on cost, quality of work, fulfilling the customers wish list, etc...make sure they are who and what you want before deciding.