I can't speak with any authority, but I can pass along what an admissions committee representative from USC-Keck said at a school visit and what I heard a Stanford adcom rep say.
He says that he doesn't get it when applicants include more than 3 letters and that it makes him think the applicant didn't check their website.
The adcom from Stanford said that if they allow you submit up to six, she doesn't see why anyone would submit fewer than six.
But, from a neurotic pre-med maintain your health perspective, it's probably best to interpret this as "no big deal...we'll just look at the first three and ignore the others".
In reality, I'm guessing/hoping that the committees recognize how the centralized application system causes some consistency in the application until we get to secondaries and that unless someone has phenomenal research letters for a research school and phenomenal inner city letters for a health equity school, we likely all just have one set of letters that hopefully convey we are a good bet.
