PTA could have gone the other way, timing the negative, then scanning that into 4K without doing much additional manipulation. It seems, if sources are to be believed, that the process was done in tandem - one for digital, one for analogue. Similar, but not exactly the same process, this is a film with a split personality, different depending on how you see it.
Why didn't PTA just scan the original IP? It would've looked far better that way. You are right that what he did was still digital manipulation. It's important to note that a digital scan of a film cell doesn't look the same as that same cell being projected onto a screen.