Ah ok, so the difference I am seeing is due to enabling ligatures. I hadn't realised that things such as "Yo", "Wa", and "fi" were covered by this

Thank you for the clarification
Edit - I just looked at Literata-Regular.ttf in FontForge, and under the View -> Combinations menu it appears to display only two ligatures: one for fl and one for fi. The rest of the changes I see on my Kobo appear to be covered by what is a ridiculously long list called "Kern Pairs". I don't know what this means with respect to "optimizeLegibility".
Anyway. Typography looks better now. That's the main thing