This is a really big item. You can have two identical homes sitting next to each other and the price per square foot will differ quite widely based on the materials used by the Builder.
A good example, Builder A uses vinyl flooring in the Kitchen/Dinette and Builder Bused hardwood flooring or ceramic tile. The wood and tile flooring cost more than the vinyl and hence the cost per sq. ft. will be higher.
Another case, Builder A uses a low end straight run of cabinets as a standard and Builder B uses custom cabinetry in several wood species including cherry with varying heights and depth creating an aesthetically superb look…
Some other product differences to consider – quality of windows, doors, plumbing fixtures, appliances, carpeting.