Where it gets tricky is that the reader might not be part of the audience intended by the writer.
It does mean "you, the reader" or "you, any random reader from my intended audience" (e.g. fellow PhDs) in articles like these.
Using it to mean "one" is a different use, in more formal talk.
(Even the audience for, say, 3b1b's explanation of what a transformer is, is niche.)