Maybe... but here is where Apple gets into trouble. There is something called chain of evidence. That means if I get convicted of a crime, the police have to prove that the evidence they have against me was never tainted.
In this case, if I am on trial and my phone is in possession of the FBI and they can't unlock it and they go to Apple... That means that Apple and the FBI created software for the pure purpose of convicting me. I have the right to request (and the courts will allow) that Apple provide the chain of evidence that was used. That means they have to disclose the code and prove to the court (and technically jury) that the code they wrote solely for convicting me has no mistakes that would convict me of a crime I potentially might not have made. IF they need my phone, clearly there is not enough evidence beyond reasonable doubt that I'm guilty. Say their software accidentally overrode another backup of a different phone. Guess what? That software is now out. Because my lawyer can ask every part of the software, what it does, how it work, and LEGALLY can get a fully working copy to be examined by my defenders.
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When your lawyer asks that question, the response will include that one of the steps is that the GovtOS is digitally signed with Apple's signing key. Doesn't matter if full details are given when one of the steps are to sign the software with a key only Apple has. Your lawyer doesn't get that signing key, the FBI doesn't get the signing key.
Iphones are made to only allow software that is digitally signed by Apple. Only way around that is a hardware mod or jailbreak.
To put someone in jail, there has to be evidence that supports it beyond a reasonable doubt. To get a search warrant or court order, there just needs to be evidence that supports probable cause.
I hope Apple's lawyers have a better argument than just saying it's going to set a precedent.