Because that's how the industry built the mobile devices regardless of the app store model. The phone is a "disposable" black box and the use cases of most users support this: almost nobody cares about accessing the file system directly for example. There's no support for anything "legacy", the form factor makes difference because it keeps most people away from tinkering with the system, all (most?) of the HW components are custom and the SW that comes with them is just as obscure. Everything relies on the cloud to the point where cutting a smartphone's internet connection pretty much takes away all the smarts. And most users don't have a problem with this, they probably never even stopped to ponder these issues.

For better or worse your PC is a vastly different beast. I'm not saying it should be like this, I'm saying it is.