Historically GDS'es like Sabre or Galileo, on the availability screen were showing the non-stop flights first and then the shortest connections. This is why airlines were pushing airports to decrease the MCT. I recall in the 90's VIE had 25 minute MCT for OS to OS connections. Today big multinationals are still using TMC's like CWL or BCD to arrange travel and they still use GDS'es. So having a shorter connection elevates the chances of selling high yield tickets (as GE or Pfaizer rather do not buy the lowest HBO fares).

I recall this was discussed on (I think) the Lufti forum and there is some sort of an audit mechanism. MCT must be set up in a way that most passengers make the connection.