Yeah, Jake’s line at the end does leave a lot of room for different interpretations: “You know, all those things that you think he missed? He didn’t. He was always there. He never really left us. I can’t prove it, but I know it’s true.” He could mean it figuratively, but you can also read it literally. We also can't forget that he’s likely meant to represent whatever knowledge the actual Jake chose to include in “Anslem”. If he decided to keep his father’s return a secret to the world, but still hint at what actually happened in a mysterious way, then that’s how he could have put it down in the book.