All other things being equal which should be less expensive to build and why: a.) a one-story, with 2000 sq. ft. on the main floor; or b.) a two-story with 1200 sq. ft on the 1st floor and 800 sq. ft. on the 2nd floor (for a total of 2000 sq. ft.)?

Additionally, both houses have full finished basements (poured concrete, 9 ft. walls); and both have radiant heat floors--in basement floor and all above ground floors.

Which one do you think would cost less to build and why?

You say all other thiongs being equal...

But the fact is that all other things are not equal when the design changes, structural elements change.

But be that as it may, since you are doubling the size of the basement with the heated floor in it, and doubling the sixe of the roof surface, the one story is more expensive to build. It will also be more expensive to heat because of greater exterior surface area to radiate enegy loss.