That’s right, it doesn’t render furiganas embedded in the subtitles specially. It should be possible for them to add a special case for Japanese subtitles and parse the files differently to recreate the furigana.
But personally I think a good alternative that would work with every language that may have weird formatting quirks like this, is to offer an option to keep the original Netflix-rendered subtitles, and only display the custom ones over it when video is paused.
That would also fix the font rendering issue highlighted by my thread which you linked.