I'm not conflating anything nor am I making a judgement on the FBI's motives. The FBI issued a national security letter that Lavabit fought in court, which I feel Lavabit should have won. The point you missed is the FBI and the judge put a bit more weight towards forcing Lavabit's hand than it did in PIA's case because of the scope and severity of the offenses, perceived or otherwise.

The FBI did not issue a national security letter in the Lavabit case. A national security letter cannot require the placement of a device to intercept communications or compel turning over encryption keys to accomplish the same. The FBI presented Lavabit with a subpoena issued by a judge.