CoachFP: Getting them warmed up is a pretty good reason. You are talking about 12U girls. They aren't going to be able to throw for five minutes and get on the mound and throw strikes. If they need 30 minutes to warm up and you have two pitchers, that means 4 players are going to miss 25% of practice.
I'm not a big fan of specialization, and certainly not at 12U. Everyone needs to learn how to field ground balls, catch fly balls, cover 2nd base, etc. By pulling the pitchers and catchers out for 30 minutes to warm up, you are penalizing them.
30 minutes to get loose and they are 12yo? I coached 12U and it doesn't take that long and any time you lose warming up the pitcher is only with the first one because the second one is loosening up while the first one is pitching. I don't understand how you run a practice but it is not that hard to warm up pitchers when you are doing BP.
The other posts regarding pitching against your own team mates don't make a lot of sense either. It is batting practice and I stress throwing strikes and mixing up pitches. If the hitters can't hit our pitchers are they going to be able to hit opposing pitchers? I think some coaches overthink this game.