Hi Janetta,
You could go to the Brookhaven Town: 1 Independence Hill Dr, Farmingville, NY (631-451-TOWN) directly and find out the detail. If you can get the plan from the builder, bring to the town in Planning Dept or call that this ph# and they will direct you.
Do you have a Buyer Agent who is working for you? If you need any help please call or email me. I work in this area and I am very familiar with. I can help you find the house you are looking for. Good Luck..

You can go directly to the town's building department with your question regarding approval and hear the answer yourself. Many factors come into play in home construction, thus not unusual to have a smaller house cost about the same as a slightly larger house.

One of the most common myths out there is that there is such a thing as an average cost per square foot to build houses. The cost to construct a house depends on the ceiling heights, complexity of the layout, amount of ornamentation on the elevation and so on. It is entirely possible that the smaller house cost the same to build as the larger one. My guess is that it is just poor salesmanship on the part of the builder.
Here in Arizona every municipality requires each lot to have a permit physically posted on the site before construction begins. If the builder made changes during construction then he will have to resubmit the plans to the city before he gets an occupancy permit.
You have to evaluate each home with the lot price and location in mind. A bigger and better located lot can increase the total price.
The most important criteria for picking a custom builder is quality and trust. A fair price will work itself out, but if quality and integrity are missing then walk away. My guess is the builder is a good builder, but a little unorganized and not so good a salesman.

Janetta
My recommendation for you is to hire a qualified home inspector!
Wiring, floor plans, plumming, are only a few of the items that most
be addressed on the inspections. Alone with your lawyer and buyers
agent they, can try to work on the price a little more.If you have additional
questions or need an agent fell free to call and direct them to me.
My Direct # 347-813-1290.
Here is my website http://fajardodelacruz.realtors.officelive.com
or my e-mail delacruz.fajardo3@gmail.com
Hope to hear from you soon.