No. No magic pips. They can concentrate solely on their station so they don't have to divide their attention. There's got to be some way to reflect that. If not in an extra pip for the system that they are responsible for, then come up with some other suggestion. But there's got to be a reward for not having to divide your attention amongst all 3 systems.
How then do you explain the multicrew slf pilot providing the ship he isnt even on an extra pip? His prescence controling a fighter isnt adding anything to the main ship systems, or making those systems easier to use in any way.