I was curious about this so I hunted it down: https://youtu.be/AaTRHFaaPG8?si=NbIe3hBSovvOQA-G&t=4483
He speculates that Wikipedia got the idea from Arbital. Insofar as I can tell, that seems to be a wiki-like website that started around 2015 -- I had never heard of it, so it might be older? That does predate this specific implementation of popups on Wikipedia, which is from 2018.
The fun context here is actually discussed in the article -- the genesis of the Wikipedia popups was a community gadget on Wikipedia (Navigation Popups) that's from much earlier. Oldest version I could casually dig up on Wikipedia is from 2007. Unless Arbital is vastly older than I think (older than LessWrong itself, which is from 2009), the chain of inspiration is presumably in the other direction. Or completely independent.
The article is, overall, about why it took so long to go from that working example to something more robust.