In college, the clock stops when a team gets a 1st down. In the NFL it does not. That makes a big difference. That's why NFL teams clock the ball after getting a 1st down, but college teams do it less often.
Now, if Iowa clocks it on 1st down, and everything is the same, the next 2 plays are incomplete passes and they have the ball on the 47 yard line. They probably don't try a FG then. As it was, they took a few extra seconds, and were able to run normal plays. The 2 incomplete passes and CJ's 8 yard run where he gets the ball to the 39 yard line for the FG. By the way, CJ goes down intentionally with 2 seconds to go instead of going for more yardage and possibly running out the clock. So, in this case, I think they did the right thing.
By the way, did you see the end of the Ohio State - Northern Illinois game? OSU has a 7 point lead with 2 minutes to go and Northern Ill does not call timeout after a running play. OSU does not huddle and snaps the ball with over 20 seconds left on the play clock. The announcers cannot believe what is happening. Then they punted with 16 seconds left on the play clock. This is the great Urban Meyer and he can't get his team to understand how to run the clock out at the end of the game. It happens to other teams.