CSS 3 transitions and animations are really no different. The reason I thought they were out of place at first is that they involve the manipulation of elements on the page, making things move and change. That sure sounds like behavior. Well, in a way, it is, but it's also presentational behavior. Links that change color on hover are ubiquitous presentational behavior, so why wouldn't it be presentational to have the color visually transition from one to the other instead of switching instantly?
Instead of thinking of presentation as what things look like and behavior as what things do, we should think of presentation as anything that doesn't fundamentally alter the page, and behavior as anything that manipulates document structure or data, or that facilitates explicit user interaction.