I have PocketBook firmware 6.3 installed and the latest nigthly version of KOReader and I do have the option to associate file extensions.
Possibly if you delete the file "extensions.cfg" the option will appear again in the KOReader configuration menu. Or edit it directly by putting "koreader.app" first in the file extensions you want.
https://drive.google.com/file/d/1CR9...w?usp=drivesdk
https://drive.google.com/file/d/1CW1...w?usp=drivesdk