Looking over the part where you imply that the MacOS App Store is the standard way to install Applications on MacOS

That is the standard way. An app that has its own custom installer or patcher/updater is by definition, using a non-standard install procedure.

But even if it wasn't, it definitely is the standard on Linux, where package managers are the norm.

The application developer grants their app the entitlements to read user files.

Flatpak works in exactly the same way.