Executive agencies almost always interpret the laws they enforce or execute, even when Congress hasn’t clearly delegated rule-making power to the agency. This interpretation is a normal part of government, and does not change what the law actually is: it’s absolutely not the case that agency interpretation has revised the Patriot Act. For example, the Wired article you link to clearly discusses the tangible records provision of the Patriot Act, which is section 215. The government interpretation of section 215 hasn’t revised the Patriot Act’s provisions such that they “are all secret now so nobody will know what section to deny until it’s to late.” If Apple had included a section 215 canary at the time the Wired article was written, that canary would have been and would remain just as effective as the one they just wrote: section 215 continues to be the tangible records provision and it has not been superseded by a secret revision of the Patriot Act.
