1) The std devs are much, much bigger than the differences in means between similar schools
2) If one school has a considerably lower average than another you're considering, you personally will likely score similarly regardless of which you choose. Chances are the gap is mostly from one school having much lower average GPA/MCAT and/or the students typically do less individual prep (like maybe the school is heavy on matching primary care).
To me it would be a massive mistake to give this any weight for most decisions (there might be a rare exception like Mizzou vs Kansas). Your personal academic abilities and background, and the SketchyMicro and Pathoma and First Aid and UWorld that you use, is going to be exactly the same. Pick the school with better location or cost or student happiness or whatever else >> step scores.