Its not wrong for you to approach everything so skeptically, but I think you have to see it from the authors perspective:

1. He clearly has an altruistic bent (he'd just returned from the Peace Corp. in Kenya)

2. He liked his position for its flexibility and variety as noted throughout the article.

I think the point of the article is that many people approach salary negotiations as an optimization of just salary. But his real desire was to be happy and money was only one component of that. The boss found ways to make him happy without meeting his salary demands.

The story isn't a story of a 'clear win' for him, its an analysis of how to approach negotiations. Salary negotiations aren't always about maximizing your salary, you can make them more flexible by maximizing for your happiness. It presents more flexibility to both participants.