Do you feel that is a flaw though? The bay valley league is ranked as the 8th best league in California while the highest rated ccs league is west catholic at 15th. According to calpreps.com
All the section seedings have some issues. Not everyone is happy. NCS seeded Bishop O'Dowd 4th behind marin Cathoic that went undeated but SOS wasn't exceptional and Cardinal Newman and Rancho Cotate..who are in the same league andsplit their games against each other (one league and one nonleague). CN also lost to St Mary's - Stockton. Bishop ODowd lost to a good Freedom and a DelaSalle. Best win for Marin Catholic was an okay Campolindo. Bishop ODowd beat a higher ranked San Leandro and had faced several more higher ranked teams (Cal Preps). Cardinal Newman beat and lost to Rancho Cotate but won its league because it it was the designated league game (the other nonleague). Rancho Cotate was ranked higher than San Leandro but Cardinal Newman also lost to them . There is an argument for Bishop ODowd to be ranked higher than all, or at least #2 but were seeded #4.
All I am saying, there is no perfect system. CCS actually has been rather innovative in many ways. They had an Open divivson for many years and have set up a system that at least those that move on to the bowl are now at least relatively representative to the best teams by enrollment size. Yes...one of two WCAL teams might be better than those that move to the bowl but it is way better than before.