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.
No, it’s not a good thing. The solution would be to use a different package name for the f droid version. That’s what’s supposed to be done. It’s not the signature or Google that’s causing the problem. It’s that there are two packages with identical names that should not be identical.