There is no proration on them. The reason the combo deals less damage overall when all of them hit is because each hit lowers the opponent's guard bar a bit (By about 3 points each, IIRC - The guard bar has 257 units to it, going from -128 to 128.).
As long as the guard bar is below 0 (the midpoint), the lower the opponent's guard bar, the less damage they take, so since each hit of Rensen doesn't do much damage (20 each, without any damage scaling), hitting with every hit will mean you do a bit less damage in your combos, since everything after the Rensen will deal a bit less damage hitting with 3 hits than hitting with 2.
Note that this doesn't apply if the opponent's guard bar has been jacked up, since as long as the guard bar is 0 or higher it won't scale damage - in that case, more hits = more damage.