Updates to the OS and applications are encrypted, completely opaque, signed by Apple instead of the original developer, can be granted additional entitlements for arbitrary permissions, and cannot be audited by anyone but Apple without a jailbreak.
When coupled with push updates, Apple already has a targeted backdoor into every iPhone anywhere connected the network.
This is a much more difficult problem to solve, as securing against that threat model requires an diverse ecosystem of 3rd-party audit/review, software, and tools.
I don't see any way of solving that issue while also maintaining their stranglehold on the platform via DRM.
What's the highest permission an app can have? Wouldn't that be the limit of the vulnerability here? Also, many permissions require manual granting, e.g. contacts, camera.
Edit: also, that could be mitigated partly by requiring user approval of any updates adding permissions.
Why do people (smart people, even!) continue to insist that this problem can be solved by technical measures? This problem cannot be solved technically. Stop it. Please. This misinformation is hurting all of us.
If you want snoop-proof encryption then the user needs to manage the keys herself, which I believe was MJG's point in that blog post. (And even then you're trusting the hardware itself not to have a backdoor to pull off the pass phrase, etc...).
At this point the techindusty should have drawn a line and fight for it.
Maybe this is Apples strategy. The want to raise the conversation but know they are gone lose this perticular case, so that they have a better position in the next, more important case.