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.
It’s not though it’s because the developers use the same package name for the f-droid and play store versions but when the play store checks the signature before installing it sees it doesn’t match and it fails if the developers used different package names for play store and f-droid this would not be an issue