Because when dealing with a compound movement, you can change your targeted muscles, and the degree of activation of those muscles, by changing your ROM, leverage, grip width, etc. It doesn't mean anything different is happening in the muscle other than the total number of fibers recruited changing.
Your chest doesn't know or care if it's doing a flye or a bench press, it does the exact same thing as far as your chest is concerned, you will just exclude the other assisting muscles with the flye, and possibly have a different response from the endrocrine system as well.