One thing that apparently happened after this story was posted
Apple issued another denial that specifically said they aren't under any national security gag orders. I suppose if you were under a national security gag order capable of making you issue denials, it could make you issue a "we aren't under a gag order" denial.
Given the report that this was closely held within Apple, maybe when Apple was reached for comment and they internally contacted "people who would know about this" they simply didn't reach the people who did know. That is, Apple issued a denial because as far as they could tell, the denial was true. If a few engineers find something like this and report it to their manager, who says "let's take it to the FBI" and the FBI says "please don't talk about this with anyone else" it only gets as high as that low level manager.
IMHO it is quite plausible that when Apple spokespeople were contacted for comment, no matter how thorough they were in looking for any evidence that this story was true, they can't talk to everyone in the company so they might simply have not talked to the right people. The question is, if true, would those right people see the story in the press and that Apple has issued and decide to tell their higher-ups so Apple gets the story straight? Or would they keep their mouth shut, and figure correcting the record now will only make things worse?