That felt to me to play the same role as "local footnotes" (those footnotes that sometimes appear not at the end of the page, but at the end of a short section or paragraph)?!
The nuance is a bit different. With what TFA is talking about with furigana, the implication is that whoever is speaking has said one word but pronounced it like another. That doesn't really make sense in English but with JP and kanji having lots of readings it's kind of a normal way to think.
So in some cases it's really no different from a footnote - e.g. in the JP version of Neuromancer there are bits where dialogue has the word for "immerse" with the furigana "jack in", and the effect is that the character has said the in-universe slang, and the base word is giving the reader a sense for what the slang means.
But if a character says "She's my friend" and "friend" has the furigana for "lover", or vice-versa, the effect becomes very different. You can think of it as one word being in the speaker's mind and another coming out of their mouth, or maybe as the character saying one thing and the author telling us another.
I'm not a native speaker, just fluent, but anyway that's how it works in my mind.
I think the way the author calls it "reading in stereo" is a very good picture. It's not a footnote or a liner note that explains the meaning of a word. Those live outside the text. It _is_ the word and it lives within the text. It's the inherent meaning of the characters painted on to another word.
