The user.config contains your preferences, including things like the last command you edited(so the list can jump to it when you open the "Edit a Profile" window), the settings you used for certain actions(like the delay between keypresses), window positions, and whether or not the application shut down gracefully.
Using two separate files would mean these values will not be synchronized between them, so some things will be different depending on which file you load.
Personally I wouldn't recommend it.