Comment by technojamin

This seems like the obvious solution to me. You don't know what the user's eyes are looking at, so making the highlighting a visual representation of what's in the viewport seems preferable than nominating a single section as "current".

In fact the final solution is pretty bad. Sure, it looks nice when I scroll down, but when I use the alternative navigation method of clicking the sidebar items, it just scrolls to unexpected places.

Beautiful article, though.