That said I have a 2012 Kobo Mini with the option in stock firmware (and an undocumented "only refresh when I choose to" setting too). Maybe there's a firmware update for yours that would add it?
What I really want is for the framebuffer to remember past pixels, so that the blacking out is restricted to only areas where there previously were pixel. I don't really mind noise on where the text was while the page is replaced, it the big areas flashing black needlessly that's distracting.
I might try out this firmware over the holidays though. If I get back into using the kobo as an e-reader, maybe I'll look at the issue myself now that it's open source, if it's not been addressed by someone already.
For the stock reader I believe this was the option I changed to disable automatic refresh entirely : https://old.reddit.com/r/kobo/comments/pbqey3/page_refresh_i...
From what I remember, mine always fully turns black then clears before rendering. Even big areas of the page that are white both before and after, there was always a full screen black flash. I wouldn't be at all bothered if it was just the areas with text that went fully black before clearing, but it's very jarring full screen.