When it comes to your personal data, Apple loves (correctly) to say "all of our user's data is encrypted, we can't access it even if we wanted to, so we cannot respond to this government request for data"
When it comes to application distribution, all of Apple's courage immediately disappears. They could say "We don't sign or control apps distributed through third party app stores, that's out of our hands, so we cannot respond to this government request". But, they chose not to. It was a choice, and Tim Cook chose an ugly, dishonorable, cowardly path.
It would be trivial for Apple to push out silent targeted OS updates to specific individuals that would log decryption keys and send them to Apple, enabling Apple to decrypt that specific user's data.
Remember, Apple is the same company that cooperated with the NSA to secretly log and feed user data to the NSA starting back in 2012, as revealed by Snowden's heroic disclosure of the PRISM program (which was ruled unconstitutional by a federal judge).
Apple's privacy-protecting image is nothing more than marketing.
One is a selling point to the security conscious user. The other they no longer need to care about because Android is now a walled garden too.
You haven't noticed that the tyrannical agencies, aka "intelligence" agencies in the west no longer white and throw tantrums about "going blind" and "black holes" etc. regarding Apple device encryption?
I do not get the impression that they just forgot and stopped being traitors.
To protect their users they chose to include a feature that allows them to remotely kill nefarious apps on all devices, regardless of how they got installed. A consequence of that is that they cannot answer government requests to kill apps with “I'm sorry, Dave. I'm afraid I can't do that”.
Was that the right trade-off? I’m not sure, but AFAIK, they aren’t allowed to add alarming warnings when users add alternative stores, so they can’t put up signs “you’re leaving the safe area”, so I can see why they made this choice.