Apple can silently slipstream applications onto a users iPhone ? That would means dozens of employees would be involved in a conspiracy with the US government. And over all the years none of them has leaked anything ? Sounds far fetched.
Also better not use a phone. Because Android and Windows Phone would have the same problem.
Of course Apple can "silently slipstream applications onto a user's iPhone". Whether they'd risk getting caught doing it (even for non-all-powerful law enforcement agencies) without a court order or for anything less indefensable than a kiddie porn investigation is less clear. (And whether the NSA would even need Apples help to do it themselves is questionable - I suspect whoever owns the baseband has as much access as you'd even need, so now you're relying on AT&T/Comcast/Verizon/TMobile to put protecting your privacy above keeping the corporation on-side with powerful government agencies...)
Apple can remotely delete apps on iPhones. They've used it to delete apps that were removed from the app store. Apple can force your phone to download the latest U2 album. Upgrading your apps silently is probably not outside their control if they wanted to.
My phone certain did not automatically download Songs of Innocence. For those users whose phones DID automatically download it, they must have enabled the "automatically add purchased content to this phone" feature.
According to my research, Apple has NEVER used the "kill switch", unlike Google: 'Google also possesses a remote "kill switch" for Android apps, but unlike Apple, it has made use of the feature before. In 2010 the Android security team deleted two apps created by a security researcher after they "misrepresented their purpose in order to encourage user downloads." Its kill switch is referred to by the company as the "Remote Application Removal Feature.' [1]
The point is they have the capability and because of your government's secret court system the general public very well may never find out whether or not the capability has been taken advantage of.
I can guarantee you that the "automatically add purchased content to this phone" check box does absolutely nothing to protect your phone from downloading and integrating data from Apple silently if they should choose to target you. And you would likely never know if they choose to target you.
iPhones by default are set to automatically download purchased content from the iTunes Store. It's a feature so purchases made on one device automatically appear on others. All Apple did was "buy" the U2 for everyone. Nothing magical about it.
To bring that up in the context of iMessage security shows either ignorance or stupidity.
And remote deleting is quite a bit different to silently upgrading apps for the purpose of spying.
Also better not use a phone. Because Android and Windows Phone would have the same problem.