At least one big difference is ownership. With lavabit, the company owned the code and infrastructure that was used in a "crime". With an iOS device, Apple has

At least one big difference is ownership. With lavabit, the company owned the code and infrastructure that was used in a "crime". With an iOS device, Apple has sold the device to an individual who is now responsible for that device. That's a huge difference. The government has been using third-party doctrine as a weak link to exploit to get stuff it wants. Apple essentially removed themselves from the situation so that they are no longer a third-party responsible for the desired data.