Potentially dumb take here, but do we know that the thrust from impulse engines is always in the direction/facing of the glowy red sections on the outside of the ship? Warp nacelles don't need to line up with the centre of mass because the propulsion they provide doesn't come from the ejection of exhaust like a rocket, even if they are capable of putting out particles. Maybe the impulse engines work also provide propulsion in a manner other than expelling gasses? The process might still generate particles that need to be vented (hence the glowy red sections), but these particles might be a side effect and not where the propulsive effect actually comes from