Teams generally do not practice "hard" during the season outside of maybe the bye week. Those practices should take place during the summer or spring. A team like Bama has the option because of its depth to run more of a mini camp in the month prior to the BCS game. ND didn't have that depth and while it wasn't a disadvantage in the season because other teams were in the same boat, it was a disadvantage vs Bama.
Not to mention when Ara was coach, the scholarship limit wasn't 85.