You are making a big assumption that the additional plays are spread over 4 hours. If your defensive conditioning is not up to par, the difference is more likely to be weighted in the 4th quarter, when what might have been a couple of "3 and outs" instead become two 10 play scoring drives.
Speaking of assumptions.....
Do you have any data on that or are you just assuming? It's possible it would be weighted more. Or it's possible that the offense went more three-and-out early on so the defense was on the field more but once the offense got going they held onto the ball more later in the game so the number of plays is skewed the other way.
Either way, more substituting on defense can likely more than make up for the difference, whenever it might show up.