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 :(