In my view, locked down desktops and web apps are just two different ways of taking away freedoms.
The difference is that web apps give you something in return. They allow you to run software without having to buy and support all the required hardware.
A desktop restricted to running apps from an App Store takes away freedoms without providing anything of any additional value for competent users.
I think the really critical difference is that Apple and Microsoft can't tell me what "apps" I may or may not run on the web but they do demand this privilege on their mobile devices and seem to be making moves towards insisting on it on the desktop too.
The difference is that web apps give you something in return. They allow you to run software without having to buy and support all the required hardware.
A desktop restricted to running apps from an App Store takes away freedoms without providing anything of any additional value for competent users.