The underlying problem is that when you pin a site to your home screen, that site gets a separate application identity and storage container[0]. SpringBoard shows it as a separate icon and window in the multitasking view and Settings shows a separate settings page for it, too.
If you squint a little, you'll notice that this sounds a little like the problem Craig Federighi cited with Xbox's cloud app. Namely that Apple doesn't want multiple apps wearing the same 'trenchcoat', so to speak. But they also don't want to actually implement the APIs necessary for an app to break itself apart in the UI and pretend to be multiple apps. So you can't have multiple icons on the home screen, or launch with different storage containers and permissions depending on what app was touched. You can't even have a dependency that gets shared across multiple apps, like what Microsoft wanted with the streaming and authentication code for Xcloud. Ship multiple copies.
Personally this still smells like malicious compliance. Apple does literally all of the things I just mentioned and has been doing them since iPhone OS 1.0. Any security issue caused by an app having two icons can be remedied by the exact same review process that Apple insists they need to be the kings of anyway.
[0] On Apple "device" OSes, each installed app has it's own sub-home directory inside the user's home directory (/var/mobile). This is called a container.
Originally the container had both the app install and it's data; but those were split around iOS 9 so that apps could write to shared containers. That's also why some apps don't actually show up on the Storage view in Settings, and instead there's a separate entry for the developer as a whole.
Containers don't exist on macOS. Mac App Store apps and iOS apps on macOS live in /Applications and write to your user home directory.
If you squint a little, you'll notice that this sounds a little like the problem Craig Federighi cited with Xbox's cloud app. Namely that Apple doesn't want multiple apps wearing the same 'trenchcoat', so to speak. But they also don't want to actually implement the APIs necessary for an app to break itself apart in the UI and pretend to be multiple apps. So you can't have multiple icons on the home screen, or launch with different storage containers and permissions depending on what app was touched. You can't even have a dependency that gets shared across multiple apps, like what Microsoft wanted with the streaming and authentication code for Xcloud. Ship multiple copies.
Personally this still smells like malicious compliance. Apple does literally all of the things I just mentioned and has been doing them since iPhone OS 1.0. Any security issue caused by an app having two icons can be remedied by the exact same review process that Apple insists they need to be the kings of anyway.
[0] On Apple "device" OSes, each installed app has it's own sub-home directory inside the user's home directory (/var/mobile). This is called a container.
Originally the container had both the app install and it's data; but those were split around iOS 9 so that apps could write to shared containers. That's also why some apps don't actually show up on the Storage view in Settings, and instead there's a separate entry for the developer as a whole.
Containers don't exist on macOS. Mac App Store apps and iOS apps on macOS live in /Applications and write to your user home directory.