The application/contract signed by each club's DOC when the applied to DA specifically required they place their best players in the club onto the DA teams. It was (and still is) online, so you can look it up. It spoke volumes about how US Soccer viewed the role of the parent/player in the actual decision making process of controlling their own development. Arrogant is a word that comes to mind.
What is not surprising is that clubs who were awarded DA did not make this clear to their members/players at that time nor during tryouts. Likely clubs also asked themselves how that provision would be enforced, decided it would be difficult, at best, for US Soccer to do so, so they ignored it. Good for them.
As for Baker Blues and other '02 and up ECNL teams, my bet is that ECNL continues to be a stronger league than DA for these age groups, by a wide margin, even in Socal.