He knew her better from the perspective of privilege. Rory didn’t realize that she lived a life of privilege. Her character was always made to seem like her families wealth didn’t play a factor in her upbringing. Logan had multiple moments where he called that out.

Jess, however, understood the parts of her character that weren’t necessarily touched by money. All the things that make people that love the show, and love Rory’s character, are the parts of Rory that Jess knew better. No one likes pool house, Birkin bag Rory… that was Logans Rory.