Both instances do read and write from/to /sdcard/koreader.
The fact that both can be installed at the same time because they have different package names doesn't mean they should be used at the same time.
The logic for that was in
https://forum.f-droid.org/t/change-p...n-repo/13543/7
Anyways, I keep both installed on my tablet and keep testing the Fdroid flavor from time to time and I didn't experienced a single settings corruption and it shouldn't happen on sane devices because settings are flushed when the app is in the backround. But there're a lot of android insane devices
For what you want I would recommend to use one of the apps that let you isolate apks using a "work profile". Here's a good one:
shelter