Here's my answer to the title question, before reading the post*:

I understand the word "agent" to refer to model I created specifically for modeling humans. The agree to such a degree that any discrepancy is almost entirely due to the ambiguity of these words.

After reading the post: I don't notice myself making the distinction you describe. Under your distinction, the way I model people seems more like treating everyone (including myself) as a complex system than treating everyone (including myself) as an agent, but I'm not sure of this.

*Well, I peeked at the first few sentences.