Yeah, we need to tweak them; they were designed for a wider browser window than a lot of people use. If they're not rendered as actual sidenotes, I think we should make them footnotes or popups.
The sidenotes also come first when reading with a screen reader, and there's no indication that they're sidenotes.
On the other hand, nice job with the alt text on the packet diagram. Maybe it sucks that the diagram itself can't be accessible, but I think you did the right thing in this case.
This has been a peeve of mine for awhile; we're going to "demote" them to pop-up footnotes when there isn't enough screen width to make them sidenotes. (In either case, you're better off than when they're in the main flow of the text).