Some schools take these 2 science/1 non-science and append them to a very personalized committee (or advisor) letter that is very formulaic (which I love because I know for a given school exactly what I'll find , topic-wise,and where I'll find it within the text) but very informative as it synthesizes the student's academic record, service, research, and clinical experiences, and sometimes some personal things about family, the transition from HS to college, etc.
Some schools are small enough that students never have huge lecture hall courses, even in pre-reqs, and they are able to garner letters from faculty in small seminar classes in advanced level material.
So, the medical schools are tilting the playing field toward the pre-med powerhouses (the Ivies, Hopkins, UVA, UNC-CH, Duke, Emory, ND, UChicago, WashU come to my mind)and some of the liberal arts colleges, at the expense of some of the big schools that don't have committee letters and where students rarely see a classroom of < 100.