The Stanford clock keeper intentionally allowed the clock to run out knowing that would allow the officials to reset the clock. By rule, resetting the clock intentionally gives the team with the ball a stopped clock situation which is the equivalent of a 4th time out in this case.
The reality is, there's no reason the clock operator should have allowed the clock to run out in that situation. All clock operators in NCAA Football games have to be trained and certified. In fact, they are highly trained and well paid for being a clock operator. The play was blown dead and the clock should have been stopped with at least 1 second left.
If Stanford's clock operator had done his job correctly, the clock would have stopped with at least 1 second while the chains moved and the ball placed and made ready for play. The Officials should have wound the clock when the ball was made ready and that should have been the half.
The NCAA needs to address this glaring problem within the rule which allows the home team to take advantage of a stupid loophole that should not exist. They should use the same rule the have in place for spiking the football which requires at least 2 seconds to spike the ball and still get another legal snap.