That is why side notes are so nice: you don't have to scroll down, you just look at the side bar. And if you just want to read code...hide the side bar! Horizontal real estate is not a big deal with 80 column code widths (you could even have two or three screens of code on one monitor still). Heck, you could render the comments with a proportional font to save even more H-space (fixed-width fonts are extremely archaic).
Programming should move out the typographical stone age into something a bit more modern.
I see where you're coming from regarding ease of hiding/unhiding comments, but I think it'd be quite hard to do correctly in user configurable environments.
In the article, I'm assuming the left column takes up a bit less space on the author's browser viewport, but it takes up about 45% of mine, while a bit of the code trails off the page.
The reason I think it works so well with physical books is that the dimensions are known and not user-configurable, so it's easier to guarantee that the sidenotes look appropriate. With free-form comments that could range from a one-line comment to large paragraphs to explain one line of code, I don't think there's a way to make sure they would look reasonable in all cases. (I could be wrong)
A good example of easy-to-read in-text notes (in my opinion) are those in Fred Hebert's LYSE [1]. They could be sidenotes or footnotes, but instead they're in-text, which makes them easier for me to read in a browser, regardless of screen size, but also pretty easy to skip over since they're color-coded and in their own box.
I think it's more of a medium difference than a book-typography-is-more-modern one. When scrolling through a web page or code, I mostly find the single-column in-text notes/comments easier to use, though I see why some people might prefer sidenotes.
Programming should move out the typographical stone age into something a bit more modern.