They are already overbooking the seats and have a list of standby passengers to fill it. They have already optimized this problem away, to the detriment of passengers in many cases!
Is empty but is already paid. That's what I don't get here. I can buy two seats, one for me and one for my imaginary friend, and the airline won't get less money. But it seems that they dream about selling the same seat twice.
The problem is they don't price flights based on cost, they price flights based on a model showing the most popular routes and recoup costs on losing flights by jacking up the price of the more popular ones. Layover flights are less popular.
The issue of skiplagging is obviously the direct result of their pricing model. And I don't see a solution for them, direct flights will always be more popular than layovers, and so more in demand. They are stuck in the position of doing what they do, or dealing with demand they can't meet with by pricing based on fuel cost instead of demand.
Alternatively, the airline may be able to have another paying passenger fill the empty seat.