The summary what written by an idiot grinding an ignorant axe against Apple.
First off, its a PATENT FILING, not a policy paper. Second, the /. summary is, predictably, a wildly sensationalized bit of bullshit. Third, provisioning has several applications.
If you knew anything about mobiles, you'd already know you don't have true device root on any phone, including FOSS projects like OpenMoko and Android. You may have mostly open access to the PC-OS side of the device, but carriers control their own network and the FCC mandates a closed baseband. There is nothing approaching an "unlimited, unfettered device," for obvious reasons.
To say that Apple is treading on your rights in designing a provisioning system used to enforce carrier feature options set BEFORE you buy the device is simply juvenile ranting.
This is not about locking down features after you buy and agree to a given level of service. It's about creating a product with features set by the provider that you have an OPTION to buy.
If you stand back, you'll realize that the smartphones that "aren't crippled" (in your view) are actually the most lame. Like OpenMoko, an open phone that can't dial. Or Android, a platform that announced its SDK and store before the iPhone, but can mange to keep up with Apple nor attract similar interest from developers or users.
When Apple is the only option, you can begin your complaints. Right now, there's no chance Apple will ever become your only option in smartphones, so stop sniveling about your ideological purity that doesn't work in the real world.