The copilot.tmc is a set of parameters that the copilot uses to fly the airplane and to control the systems. This is mainly the mass of the airplane, wing area, flap airspeeds, gear extension speed and things like that. It also defines what the copilot knows about the autopilot in the aircraft and what buttons it can push or modes it can use.
But the copilot also takes care of the throttle mixing. So if you only assign Controls.Throttle it diverts it to single engine throttle Controls.Throttle1 or multi engine throttle Controls.Throttle1, Controls.Throttle2, etc. depending on what the aircraft has defined in the copilot.tmc file.