Unless you believe the NSAC could somehow get into their magic Silver Delorean and go back 8 months to double check Margo's hands in the dressing room, the commission "officially clearing" Margarito was just a way for the commission to cover its own ass. It's unknown if Margarito loaded his gloves in this fight, or any other for that matter pre-Mosley, unless they admit they did something shady.
Margo can be quite inconsistent at times, he looked a different fighter in his last two fights, i don't know if foul play was the reason but i would give cotto a good chance of revenge. A lot would depend on which Marg appears