He was a sysadmin for three months. He never claimed to have firsthand knowledge of this tool. He found the slides on the intranet and jumped to conclusions.
Where did Snowden himself claim firsthand experience? Nowhere. That sentence is the author's conjecture. It's shoddy journalism.
This is exactly the same as how the slides saying that the NSA collects data directly from the companies was misinterpreted by WaPo to mean direct access to all the companies' user data. I suspect Snowden jumped to the same conclusion when he came across those slides while sysadminning, and that's why he's in the mess he's in now.