Overview
When Morning Flight calculates a 5-1/2 x 8-1/2" business form 2-up, it assumes you'll be using a single original. In other words, the same form imaged twice to double the yield. The press doesn't care whether the two images are different - makeready and run costs will be the same either way. Ditto for postpress. It's prepress where costs may differ, depending on how the film is generated.
Imagesetter
Film either outsourced or produced on an in-house Imagesetter is commonly done full size. That makes the number of originals irrelevant. It doesn't matter whether you run the same form 2-up, or two different forms side by side. Morning Flight will charge for a full 9 x 12" Film Unit in either case.
Camera
Here, things get murky. Most shops still using a camera will either cut the film in half before shooting an undersized original, or shoot two small jobs together and cut the film apart when it's dry. Others may use a full sheet no matter what. Take a look at the Run Cost window below. You'll find Morning Flight squarely on the side of frugality, with film costs and film units cut in half. The program assumes you'll step-and-repeat the image to get 2-up on the plate.
In time, with more and more imagesetters coming on line and replacing cameras worldwide, this won't be much of an issue.
See also