Maybe problem is a big word. It just happens that the same package name is shared across 2 different build types. The issue is with Google lack of clarity of why an install failed.
I do remember both bug reports and forum questions related to this issue, but can’t locate most of them. Just a sample in Couldn't install koreader last version · Issue #6698 · koreader/koreader · GitHub
Some people discover the app through F-Droid, catch a bug, report it and receive the answer: fixed in today’s nightly. Since fdroid releases the package on tagged releases some users might be tempted to check if their issues were, indeed, fixed. This would lead to the usual dance:
What’s a nightly? → Here’s the nightly http://build.koreader.rocks/download/nightly/ → APK failed to install → open bug report.
That could be solved with a different package name (as others app have, for instance Librera). People downloading from github could still use their f-droid client for other apps without the github package appearing as installed. F-Droid users could check if the last nightly fixed a bug without having to uninstall the APK first.
Keep in mind that KOReader is a very niche app, so the total number of users affected shouldn’t be too high. It just happens that we’re not in Play Store (and we won’t) and F-Droid is the easiest way of getting the apk installed on Android. Also the F-Droid build requires less permissions and is a bit more secure, so I would recommend it for most users that don’t want to be on the bleeding edge.