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Because the apps that are considered part of the OS are tightly coupled to the OS itself, and often those app updates are intended to showcase new features of the OS that they want developers to take advantage of. Things that are considered standalone apps like Logic, etc. get updates through the App Store like other apps.

Things like "new emojis only in the new OS version" are used as an incentive for people to update, I believe.

Previously I would have thought they could be separate but as of Catalina it’s entirely possible that all their stock apps are part of their protected volume (and therefore not updated in any normal way). The Applications “folder” is a virtual view merging multiple directories on disk.

They usually release new versions of their apps, including Safari for older OS versions too.