Essentially the apps have same package name but different signatures and the app store that installed it should be the only one to recognize and update it.
But Google is likely trying this dark pattern to sway people away from F-Droid or alt stores by making users uninstall these apps and install it from the Google Play Store.
It’s been going on for a while and is annoying af.
This is an f-droid problem. If they use the same package name, they need to use the same signature. That has been the case since long before f-droid existed.
They could just build apks with alternate package names and this wouldn’t be an issue.