Ebooks: I use Calibre locally and Calibre-web on the server (read-only metadata db, I overwrite with the Calibre version as tagging, etc is far easier on desktop).
You can connect Koreader to Calibre-web and until maybe a fortnight ago you could jailbreak a Kindle and use Koreader instead of the default software. Now you’ll need to manually move files over, or use the email-to-Kindle option (probably a bad idea, but I expect Amazon can tell if you’ve side loaded pirated content anyway). Nowadays I buy from not-Amazon sources, strip any DRM and send it over.
Manga/comics/graphic novels: I use Kavita on the server and I use comictagger on desktop to fix the metadata.
I’m happy to use different set ups for the different types as they’re quite different experiences and specialist tools work better.
Yeah, I hate those little dots and I inevitably jump through the hoops until I’ve clicked enough things to make them go away.