"We can be legally compelled to give up data we have" and "we thought letting people have custom kernel modules was a bigger threat" are not particularly incompatible with "we design things so we don't have keys to your data we can be compelled to give up" and valuing people's security. (I am not a fan of the latter, to be clear, but there are reasonable reasons you could argue for it.)
But yes, I would probably, at the moment, bet that if the NSA can sign a custom iOS build on consumer hardware, Apple doesn't know about how, both because that's a very hard secret to keep, and because you'd see a massive uptick in people avoiding Apple devices in governments that might be of interest to US intelligence if even a rumor of that got out.