The government obtained a 2703(d) order for the stored non-content data of a particular user (suspected to be Snowden, but redacted from the court documents). They then obtained a pen register order, for real-time metadata about that same user. Lavabit told them they couldn't comply, so the government sought to use the 3rd party assistance language in the pen register statute to compel the company to provide its private SSL keys. The government then followed up with a grand jury subpoena and Stored Communications Act warrant specifically seeking Lavabit's private SSL keys.

So, no. The warrant the government obtained was not specifically for the data relating to Mr Snowden, but rather, was for the SSL keys.