I don’t think this actually physically deletes the app, given that it’s back once you reset the phone. It’s most likely just hidden/deactivated until you “reinstall it from the app store”.
Actual updates require the app binary/bundle to be mutable.
Not the OS-included ones, afaik. Some Apple apps are through the AppStore normally, which can be updated independently (i.e. TestFlight, despite its deep hooks).
Why did google break out Google Play Services as a separate app, was that when they started integrating more with third-party android phone suppliers, and they didn't want to have to wait for OS upgrade cycles from slower-moving companies?
Probably they originally did it because Android has high-assurance embedded use-cases (compare/contrast: Windows IoT Core) where you want to strip out everything possible from the attack surface.
But mainly it's because base Android (AOSP) can be arbitrarily modified by the OEM; and Google doesn't want to have to trust installations of Google Play Services that have been arbitrarily modified by OEMs.
(Especially because those versions would likely all act differently-enough from one-another that they would be forced to loosen their server-side, network-traffic-fingerprint-based "authentic Android device" detection that allows them to ignore/block bots pretending to be Android devices.)
By shipping Google Play Services through the store, they can ensure that, on devices that run it, it's exactly the same code for every device that runs it, with no OEM alterations. (And they can also include various checks to reject devices that would try to alter that code at load time. This is the real reason why e.g. Huawei devices are blocked from using Google Play Services — they try to patch unspecified parts of the Play Services code while loading it, "breaking the integrity of the platform" from Google's perspective.)
Man, that's contrived. Really its simple: Google seperates out Play Services so they can harvest user data from virtually all Andoid devices. It lets them market Android as OSS while still reaping the benefits of closed source data scraping.
Google can harvest data from "virtually all Android devices" just by offering Chrome, Google Search, and Gmail as apps. Almost every Android user has at least one of those apps installed. They don't need Play Services itself to spy on you on top of that.
derefr cited one reason but there's another that's relevant to this thread: updates. In the Android model handset manufacturers and carriers decide when (or if) to ship updates. Google distributing their apps through the store gives them a way to roll out new features to a reasonable portion of their user base.