"Before I accepted this pull request, I would ask you to do a lot of refactoring. However, it's too complicated to explain in comments on the diff. Why don't we sit down and fix it together?"
Then explain your reasoning for the overall changes and each smaller change face to face in a pairing session (or series thereof).
Agreed: this is now an in-person conversation where you have an opportunity to help your colleague grow.
I have to say that I find it odd that you spent any time at all re-writing this person's code. If I was your manager, that is not what I would want you to do.
Further, reviewing code over 400 LOC _total_ is generally a waste of time (never mind a single method larger than that.)
"Before I accepted this pull request, I would ask you to do a lot of refactoring. However, it's too complicated to explain in comments on the diff. Why don't we sit down and fix it together?"
Then explain your reasoning for the overall changes and each smaller change face to face in a pairing session (or series thereof).