I don't exactly see anything "conspiracy theory" about the fact that the US Government actively trades, harvests, and uses public and private information of it's citizens; much of which it gathers in less than legal ways to use for their own benefits. Not to mention that the US Government has and continues to operate in a two-faced manner in regards to the American people; the Public Face will say one thing, while the private face is off assassinating leaders of countries and giving away weapons to armed insurgent groups to fight our enemies under the table, or did you forget about the Cold War leading up to today? There's nothing conspiracy theory about that, it's just how the Government (and honestly any country's government to be honest) works since we've given up a lot of freedom and control (particularly in the last decade or so).
Nor is there anything fairy-tale esque about a private company, whose sole goal is seeking profit participating in the largest economy on the planet; information. It'd be absolutely idiotic for a digital goods company NOT to have some form of information selling/buying these days. Nor is Apple a shining example of a company to begin with, since they've done just as many unethical and borderline shady things as any other profiteering company.
Though I will somewhat applaud Apple's efforts, be it because they don't want the government snooping in their information trading or simply because they don't trust the US Government not to screw them over (let's be honest that alone is a good reason), it's still a decent effort; hardly philanthropic, but commendable at the least. They're a global company not tied to the US in any significant manner besides a sales region (they use a holding company outside of the US To avoid Taxes like most large corporations these days).
Unfortunately there's the other-side of the coin where Apple becomes the premier product for the pedophile, terrorist, and/or other unsavory characters, which I suppose isn't a bad thing if you're trying to sell more product since the Apple
sheeple will still buy it anyways. Though fairly true (I mean if you have a device that's safe from the government thanks to the company, why wouldn't you use it for illicit dealings?), the above statement is mainly fear-mongering and political BS some senators and politicians are using to try and force Apple to concede to the US Government.
Also I'm not entirely against Apple holding out against the US Government (I'm mostly for it, again I think the case study they chose to fight them with is a bit poor, but the message is still there), but I doubt it's from sort of philanthropic place. If anything it's because Apple has leverage with this and it benefits them in multiple ways.
I'm not a programming guy by any means, but as the system is laid out I don't see why the software couldn't be manipulated in that fashion. Basically Apple's SE is just a enclosed network bus between specific chips specifically for encryption purposes controlled by software; much in the way Toyota uses an entirely separate communication bus between the ECM & Immobilizer System that is not actually connected to the OBDII port and can only be accessed via software in a scantool.
Was thinking about this a bit when snowboarding today.