A lot of people already see traveling as a big hassle and they feel they have been nickel-and-dimed by the airlines (no more hot meals like back in the day), they are groped and blasted with X-rays by TSA as if they are some tiny terrorists. (This is regardless that there are 2 separate entities involved, people see it as just one traveling experience).
So most people will do this ticket hack even if it saves them just $5, or even just out of spite ("You made me jump through hoops? OK, now you sit and wait for me, haha!" kind of reaction). I am not justifying it or saying they are right, just illustrating the possible thought process.
Now from a market point of view, airlines are trying to solve this insanely complicated problem on how to maximize their profits from all these seats on their flights. It is almost like trying to do central planning on an economy of a small country -- this seat on this flight should cost X because we think demand for it is Y, unless demand changes and then we can increase the price, and then there are different legs, through different hubs, other partner airlines that try to do the same, it is just so complicated. So they end up creating these inefficiencies with inadvertent arbitrage possibilities. And people are taking advantage. Apparently they know about it and they are trying to put all kind of threatening legal mumbo-jumbo in their fine print. But they can't enforce it.
I think as more people start finding out and doing this they could: 1) ban customers in the future, 2) make them pay a fee next time they purchase, 3) lobby the govt. to declare this a grave security concern and make TSA chase these people down 4) try to adjust their pricing and fair structure to do away with this inefficiency.