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.
I have experienced it for at least 5y or so, back when I ran CalyxOS. It would try to override the sim tool at every opportunity when calyx used a custom version. With GrapheneOS, I have always (3y) had a stub apk to give me the preview picture in gCam without requiring gPhotos, and it bitches and errors constantly if you don’t turn off auto-updating. Tasks.org joined it recently since I use Obtainium (not f-d); it’s been happening with quite a few apps, just Tasks has been out of sync for the Github release vs play store release a while now.
Android knows if an apk is installed from the ps or not, this would be a two-line if-statent fix. But there’s no incentive for them to make using alternative stores/methods work better than the bare minimum, so they don’t :(