If I were to guess it’s the lost of potential revenue, that empty seat could very well mean another traveler from the middle stop to the final stop, which they could sell for more than the original layover traveler.
So let me tell you I won't make that flight and give me $10 back while you can resell it. The pricing scheme here is the problem, not the way it's being used. Unless they're being reimbursed by the destination cities for the number of people disembarking from each flight, there's nothing about the final leg that makes them money.
Well yes, but that is very much their problem. The "lost revenue" is the direct result of their own pricing structure.
Their circus, their monkeys.
They also save by not refunding an oversubscribed seat too. Win win win for airlines.