It's got nothing to do with incurred cost. Goods and services are not priced at cost + margin, they're priced at whatever the market will bear.
A->B is a higher demand ticket than A->B->C, so the market bears a higher price for that ticket. By getting off at B, the traveler has "stolen" the difference in those two prices from the airline, as the airline would have charged the skip lagger or another direct flight customer a higher price.
Ya it's an interesting economic puzzle, given the unique nature of the airline business.
I think ultimately the incentives work out to exactly where we are, airlines will simply ban travelers from their services when skiplagging is discovered.
There's no reason to offer services to travelers who pay less.
A->B is a higher demand ticket than A->B->C, so the market bears a higher price for that ticket. By getting off at B, the traveler has "stolen" the difference in those two prices from the airline, as the airline would have charged the skip lagger or another direct flight customer a higher price.