It appears that the cooldown reduction that McmmoBonusPlus gives is actually reducing it to the amount it lists rather than by that amount. If the base cooldown of Super Breaker is 300 seconds, the 2nd rank was reducing it to 100 seconds. Now I have the 3rd rank, and it is reducing it 150 seconds. I have not tested it with the 1st rank, but I can only assuming that it was reduced to 75 seconds rather than to 225 seconds.