(not on balance/design team!)
It's the same reason Zoe's E does true damage. If the ability double-dipped from armor, even someone with no bonus armor would take way less damage due to innate armor scaling. If you did 100 damage to someone, post-mitigation that's 60 damage on most carries with no armor; just scaling
If his E transferred 100% of the post-mitigation damage (I really don't know, I haven't played him), then his E would deal 42 damage instead of 60 due to having to go through armor mitigation again.
The alternative would either be to have the second hit apply pre-mitigation damage from the first (this is how Zed works) or to deal true damage on the post-mitigation of the strikes during the E.
I prefer the latter model because it means if you have a lot of armor or you simply use a temporary steroid to reduce the first hits, you actually feel like you did something skillful.