The do-it-yourself screening for secondary applications is a tax on those with more optimism than brains. That said, the real reason is not to miss out on the diamond in the rough: odd major, below average numbers but extraordinary life experience, world-view, communication skills, etc that aren't measured in numbers (and this is not code for URM). It provides a certain diversity (not URM type diversity but another kind) that you don't get when you cut by the numbers on the first go-round.
I knew a guy who was denied a secondary and had his advisor petition on his behalf for reconsideration. He got the secondary, and long story short, he was admitted and graduated AOA (med school honor society = top 10%) and matched very well.