It could also be exactly what they say it is: a way to prevent the abuse of local storage for tracking.
Isn't the new policy for local storage being copied from an existing policy for cookies? How can they switch to cookies?
In the linked article it actually mentions that this policy is being widened from cookies to the rest of script-writable storage.
They could restrict these APIs to "installed" web apps via the web app manifest file, if they were to adopt that. Maybe they will in the future, but for now they've just made web apps far less powerful.