Is the government waging an out-of-sight fight with Apple on encryption?

Fortune:

The Justice Department and Apple have been locked in a bitter fight for years over the company’s encryption system, which allows consumers to prevent anyone —including law enforcement—from opening their devices without permission. That’s why a security story this week should be getting more attention than it has.

Titled “Yup: The Government Is Secretly Hiding Its Crypto Battles In The Secret FISA Court,” the story appeared on the well-regarded security blog EmptyWheel, and suggests the Justice Department is using a legal backdoor to force open software backdoors at companies like Apple.

I don’t know enough about the issues involved to answer the question in the headline but even the appearance that this might be actually happening sets my teeth on edge.