Well, as per what I understood, yeah, you can have separate model folders for different models (EX: 777 with different model folders for PW, RR, GE etc). Even you can have multiple .air files
All that really matters is how you present the data to your aircraft.cfg. If you want a 787 with Trent 1000 engines, and a custom .air file, simply make different folders for the different engine models (EX: RR Trent 1000, General Electric GEnx), and their model.cfgs. Later, you can add in the folder name of models as you want, and along with it, you can even alter the sim entry (for .air) of your choice in the aircraft.cfg.
Hope it helps
(Edit: Long story short, it works eitherways. You can add in different model folders OR make separate aircraft folders. Eitherway, it won't affect FSX/P3D)