I understand your point. There are two perspectives: 1) The airline wants to sell seats whichever way it sees fit; 2) the passenger wants to arrive at their destination whichever way they see fit (on a nonstop flight, via the cheapest itinerary, with maximum RDMs, whatever). There is really no easy rationale in airline pricing; however, since the airline provides the seats, it sets the rules.

Now, at the airport, if they need your JFK-SFO seat to accommodate overselling or for what other reason, I'm sure they'd be happy to swap it with a JFK-LAX one. By all means try it (I would). But in advance, barring any unusual circumstance, your chances are slim that they would agree to SDC with no fee/penalty.