I agree, but I also disagree. There is a lot of discomfort that has nothing to do with long-term physical damage to your body. The author takes the distinction for granted:

> I’d have stopped if I felt like I was truly injured

I think what the author is talking about is that we start as children from a position of trusting discomfort unconditionally. It distresses us, and we avoid it. Through experience, we learn that that the distress that many types of discomfort causes us is disproportionate, and we start to react to it differently. We even learn to associate certain types of discomfort with the reward of hard work. If life doesn't force these experiences upon us, we have to get them by choice, or else our lives can end up overly constrained by discomfort that we never learned to put into context.

But you're right as well. In the gym, people first learn what their bodies can do when they use emotion and bravado to unlock levels of effort and discomfort they had never experienced before. As they gain that ability, they also learn to moderate it, to use it wisely in the context of how their body responds to what they're doing with it. The first without the second is dangerous, and the second without the first is constricting.