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This is all just opinion here:
I think you would still see the righty do better against lefties on *average* not because of a code for the handedness directly but rather because pitchers tend to have this same system of having higher ratings against one type of batter. Most pitchers have slightly higher values vs. their same handedness so the leftie batter might be facing the same pitcher but be put up against a higher rating set. Not all pitchers follow this trend but on average the leftie would see higher ratings vs. LHP so he would suffer somewhat.
For both pitchers and hitters you have guys who don't follow the handedness trends so I don't think they would code a hidden bonus in. Instead I assume it is already figured in through the split ratings of both hitters *and* the pitchers.
Does that make sense? The way the game generates players is to have (typically) higher ratings against one hand and lower vs. the other according to what they are and this is for both pitchers and hitters. If you were to create players completely from scratch I imagine you would need to account for this then and follow the same trend. If however you are using created players there is no need to touch things.
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