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.
Why would anyone who actively chose to install F-droid, reinstall their apps as Play Store apps?
Fedilab and Thumb-key are not free on Google Play, I would reinstall them there if it was possible