chidori increases the penetrating power of the shinobi's hand.I didn't say that Kagutsuchi didn't have piercing properties, however, you cannot make something more penetrative by adding a less penetrative property to a more penetrative attack. Add a nail onto a needle and you don't have much going for you, same goes here, Kagutsuchi can have piercing properties but they are inferior, thus Chidori is doing the penetration/piercing, not Enton.
chidori on enton would increase the penetrating power of the enton.
enton penetrating power >>>> hand penetrating power, enton chidori penetrating power >>>> normal chidori via the hand. It's the same principle as raiton sword is much more penetrating/sharp than a normal sword. The chidori enhances the thing it surrounds.