I wasn't expecting to see that at all! Funnily enough that was an ultra hard version of her saved for the postgame in development (one of the three hardest in the game, even!), so the game must've picked that encounter instead!
Good job on beating her for sure, but the City encounter is definitely an easier one. The Boxman in the Dead City is guarding a house which you'll need to give an item to him for too. I'll give a look at the things you mentioned, and a new build should be up in the next day!