What sadiqhassan said. There is no way around this as this is intentional for inventory management purpose. If there is no S inventory for your routing, you cannot purchase S fare tickets. The fact that it is available by segment is irrelevant.

The reverse could also be true where S is available for JFK-LAX-OAK, but not JFK-LAX alone. No, you cannot book JFK-LAX-OAK than delete LAX-OAK as they are married segments. Attempt to delete one will delete all married segments.