The factors are built into the stats.
That is a great macro level chart, which ignores individual game and team circumstances.
For example, if a team is down by 2 with 3 seconds to play and it's 4th and 1 from the opponent's 10 I'm sure that we can all agree that you ignore the chart and kick the FG. Thus, we can agree that the chart is not a reference to be followed in all circumstances.
In the case of IA vs. WI, that was clearly going to be a very low scoring game given the nature of the two teams, wind conditions, etc.. I'd argue that a FG in a low scoring game is arguably more important than it would be in a high scoring game.
You also have to take into account your team's attributes. Canzeri is not a great short yardage back, and Daniels is ineffective right now (either due to injury or because he just isn't that good). That made a run on 4th and 2 a suboptimal play, which the coaching staff saw as well as they went to the pass.
I'd argue that going for it on 4th and 2 if you had Shonn Greene on your team makes more sense than if Jordan Canzeri is your RB. Of course that's not on the chart, is it?