Yes...the game takes care of it...for HITTERS.

It doesn't take care of it for pitchers (except when they are hitting).

A pitcher with 1 acual inning pitched but with great OPS (maybe a PB 8.8/9.0) will have his stats for that inning used for whenever he is pitched. If he is used as a starting pitcher, he will be given 30 BFA and have his stats used for the entire game even if he pitches a 17 inning shutout. You could also use him in relief and even if he were overused or very overused, his performance will still be very good.

I'm just suggesting treating limited use pitchers similarly to the way the game treats limited use hitters.