Looking at the results in the video and the short discussion in the comments it again looks like generally speaking there is no winner in the performance debate between JS- and CSS-animations.
Except for the synchronization problem all demos shown seem to have very comparable lag (or lack of lag) with both technologies on the actual animation. And that's what the user will eventually see.
Ultimately it still feels to me that performance is not that big of a factor in deciding between JS- and CSS-animations and we are (again) very much nitpicking about something without a big influence on the user-experience (not saying that performance is not important. But between JS and CSS it seems to be the same difference.). It's just the implementation that affects the performance significantly (As the 5 DOM-elements vs 1 DOM-element shows).
In the sense of Paul Irish's summary the decision should rather be if I need to build a complex animation with physics, separate timelines etc. that will be way easier to get right in JS or if I want to build a "simple" animation where the easy to understand, declarative syntax of CSS will make me and my coworkers happy (At least until the web animations API gets ready for production and we have a whole new topic to get worked up over). Performance being a smaller factor determined case dependent and fixed if necessary.