You lose nothing of the official Kobo software when you add the alternative readers, in fact they are usually launched from the Kobo interface just as if they were another book.
https://www.mobileread.com/forums/sho...d.php?t=226456
Both CoolReader and Koreader use File Managers and both can be set to read "hidden" files and folders. That way you can hide your library from Kobo's processing and database. I keep ~ 7000 ebooks on an external uSD card in my AuraHD 3.1.1.
Luck;
Ken