I'm pretty sure it is based on the physics. In theory, real life CUP cars are going to run faster laps than GNS cars and GNS cars will run faster laps than CTS trucks.
So, to answer your question, you can use any of the 3 (CUP, CTS or GNS) MasGrafx formulas you want on whatever physics you want. In other words, if you have cars with ".cup" in their file name, you can still apply the MasGrafx formula for CTS or GNS. The cars will be rated and work just fine. The difference will be in how fast they run.
I'll end my answer with the disclaimer that I do not know this as fact as I do not know the author of these formulas and what methodology he used in creating them. This is just in what I have seen in testing that I did many years ago.