I experimented a bit today with the optimizelegibility option and the word-spacing patch created by Jackie (I also installed John's improved hyphenation dictionary). Previously I'd always avoided using the optimizelegibility patch because I prioritize fully-justified text over ligatures. At first I tried with the default -0.05 setting and still had some issues, though definitely fewer than before; I then gradually went up to -0.09 and it seems to be working quite well now; I don't know if it's disappeared completely but it's definitely reduced to a point where I see it rarely, which is good enough for me.
It's definitely great to be finally reading with kerning and ligatures in kepubs
Jackie, thank you very much for your work!