I think you're missing the forest for the trees here. Without those NCS rules, one of Moreau, Redwood, Dougherty Valley or Clayton Valley Charter wouldn't have made Norcals because only the top 3 seeds from each division qualify. Do you want a worse team to advance instead?
I DO think NCS needs to rethink how they rank teams and have it much more based on how they're going to rank them at the state level. Having Open teams ranked below Division 1 teams is a bad look, and I blame NCS for determining the Open teams based on different criteria than were going to be used for Norcals.