Also:
Pinch hitters.
PC/pull setting allowing your pitcher to face more than one batter.
Inning available and game situation.
I only use specialists when I'm comfortable with the pitcher facing RHB and LHB.* Very often they're going to face more than one batter even if you set 5-5 5 pull. Just use it if you want to be as sure as possible that they'll have the platoon advantage for at least one batter.
Now, if your specialist is the only guy available for an inning when you need a reliever, he's coming in. If you're out of other relievers, he's coming in. If it's him or your Long B, he's coming in. You take your chances.
*If the pitcher is so crappy I'm afraid of letting him pitch without the platoon advantage, I'm setting his role and inning available to keep him out of important situations as much as possible.