If I had to guess, I would say that the in-system and in-combat drives are the same system, with either more of the drive system being active or the drive system being operated at a higher power level (or both) for in-system travel than in-combat travel being what distinguishes in-system from in-combat propulsion. The exhaust plumes are the same (or very similar) colors for both in-system and in-combat propulsion and are emitted from mostly the same locations on the ship. Neither the in-system nor the in-combat propulsion systems appear to follow reaction-thrust rules particularly well, and at any rate ships do not appear to be expelling mass at any significant rate, at least under the current game mechanics.
I would suggest that Starsector's in-system and in-combat propulsion system is more along the lines of something which accelerates a ship to a given speed when the drive is provided with a certain amount of power; the lower in-combat speeds can be justified by the accelerations required for combat maneuvers, a need to reduce drive heat generation to allow the ship's cooling systems to keep up with weapon and shield heat generation and perhaps reduce the ship's heat signature to allow ECM to be more effective, a need to free up power for the weapons and shields, or some combination thereof.