IMO the difference between A and B is very small here.
It is said that pitchers "use their most effective pitches more." However, since the engine sims plate appearances and not individual pitches, what that means is that the overall pitch rating that is used by the engine is a weighted average of all the pitches, and the 3rd-best pitch carries a lower weight than the best two. This return diminishes even more for P4 and P5.
By the time you get to the 3rd most effective pitch, it's carrying only a small percentage of the influence the pitches have on the sim, and then, IMO, pitches don't have all that huge an effect on the sim, anyway (compared to control, splits). So, while my gut says A, the difference in my opinion is probably miniscule, no more than 2% and probably less than 1%.