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.
Samsung just says:
Can’t auto update Installed from Google play store. And Can’t auto update Installed from Aurora store.
You can easily see from what store an app has been installed in android.