I'm thinking that limitations in their pricing algo make the seats non-fungible. Maybe they just reserve some % of seats for connecting flights and calculate A->B pricing independently from A->C, figuring it's good enough as long as customers don't exploit it. And if the seats were fungible, the price fluctuations for A->C might be wacky, like staying at $800 until A->B is sold out.
Maybe they could do this with... pricing. Like charge LESS for one leg, instead of more for both legs.
And would they complain if the customer didn't show up for the entire flight?
This seems more like "protect my crazy business model"