I have no idea what's happening with night mode on the Elipsa 2E, but, yes, it's a known issue.
(c.f., the tail end of
https://github.com/koreader/koreader/pull/10719. My best guess is that it's an issue specific to the MDP invert @ 8bpp, which is fairly strange, because IIRC, the working buffer is always RGB32).
In any case, not something I can fix without access to a device, I've exhausted all I can do via remote debugging (i.e., as far as I can tell, it *should* work, but it just doesn't).