It's not that easy to get to a 4:1 ratio. I wouldn't downplay that jump like you're trying to do.
PPG isn't a quarterback statistic at all. That's a team statistic. If the run game and blocking improves and contributes more, then PPG improves. The offense as a whole was more experienced in 2005 with the Oline finally becoming upperclassmen.
Beck was sacked a lot less too as a senior. That's because he was getting quicker releases that frustrated other teams pass rushes. TCU who had a top defense that year was basically beaten singlehandedly by Beck's quick releases and pinpoint accuracy. There's no question that the senior Beck was an elite quarterback. I don't know if there was a better QB in the nation. As a junior, he was also good, but not elite. That jump into the elite category happened between his junior and senior years. It's also much harder to jump when you're already very good.