The difference was that in the past (i.e. in the era of run-heavy schemes), great offenses helped create great defenses. Long, slow drives wear down the opposing defense, while giving your defense time to rest. All other factors aside, your offense got better as the game went on, but the other team's did not.
Also, slower plays and a continually running clock means that there are fewer plays in a game, and in the season. That helps the defense avoid injuries. Admittedly, the running clock aspect of this will lessen as our offense finds balance, and option offenses are MURDER on QB's.
This offensive system doesn't help the defense.
Also, the article doesn't give meaningful stats. Points per drive, yards per drive, and time of possession per drive are far more meaningful than of and ypg.