Yeah, you're right. This is the non-technical part of being a leader that I really struggle with. I'm much more comfortable "leading by example" and modelling behaviors and much less comfortable with how to frame a discussion like this.
Much of my company and field is full of nerds that are a bit outcast (including me). I hate the overuse of the term "bullying", but I'd say that most of the people I work with daily weren't the most loved kids in school.
So I don't want to add "boss thinks I'm doing a bad job" anxiety on someone by telling them that they're not matching my expectations. And If I put myself back to being 3 years or so out of college, I was probably behaving the same way, and maybe time to figure it out is what he needs.
My grad advisor was a real not nice guy, and even after all these years I still don't really like him. But he was what _I_ needed and my reaction to his pressure was to become a much better problem solver. I know I shouldn't act like him, but I haven't had many great role models in how to talk to someone about their performance.
I want to him to get the message that "he's smart and I know he'll figure it out" and not the message that "he's a bad employee and that he needs to start worrying about being let go in this bad job market"