>What I don't understand is how Apple will track the new 5% commission for web distributed apps.

My guess: since all apps will need to be notarized, even web distributed ones, your phone will phone home to Apple servers when you first launch it (and periodically afterwards), to verify it isn’t in a revocation list. That will allow Apple to track unique installs and then bill the Apple developer account based on pricing data reported by the web distributor as part of their separate agreement with Apple.