It is the burden of proof that is operative here. The procedures of the justice system versus the procedures of Title IX are different in ways that reflect, are set by, and are in proportion to their different burdens of proof.
As I already admitted, though, yes, there are problems both ways. Ideally we'd never have false positives and we'd never have false negatives. That a guilty person will always be punished and an innocent one will never be. When either of those happens, that's a problem. And maybe there's too much of both.
But you can't guarantee that (upon reviewing both the justice system's risk of false negatives and Title IX's risk of false positives) that the net epidemic leans in favor of "too often the ladies lie." It's unfounded, for example, to say there are more women lying about these crimes than there are unconvicted men who really did commit the crime.
And until we find a system where both false negatives and false positives are rare, justice means balancing the protections for both groups.