I don't think that there is any code in the sim to change performance based on lineup protection. However, especially in progs, that doesn't mean it won't matter. A better lineup will tire starting pitchers out faster and score more runs. That's going to get you more plate appearances against the deeper portion of the bullpen and/or more fatigued pitchers, which is going to get your batters some easier at-bats. That makes them look a little bit better. I've definitely observed this effect in progs in the past. Until it folded, I got through the first half of the '90s in a prog with Bonds, Galarraga, Paul O'Neill, Tony Phillips, Biggio, Chris Hoiles, Caminiti - a deadly lineup. There would be 10-20 games a season where that lineup would just explode for 15+ runs after pushing the starter out early. Everybody in the lineup probably averaged at least a hit more than they normally would in those games. An extra 10-20 hits per season is probably about 15-30 points of batting average added on. Add in a few walks, or at least some XBH, and it looks like a big performance improvement.