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.
Actually, I had it just the other way around. I had an app that had an old, orphaned version on F-Droid and a newer one on Play Store, so I installed the one from the Play store, but F-Droid desperately tried to update it constantly, always failing, always spamming me with messages about it