I would think it's just the opposite. Routine and unimportant correspondence is signed with an autopen. Official documents and commendations would have to be signed personally.
In most instances, your take on the matter is correct. An underling would obtain autopen signatures for basic correspondence - and even some commendations, citations, and awards - to non VIPS. For a sitting Senator, Congressman, or most other VIPs? You had better believe the Secretary would sign the document personally.
Yup. A Silver Star is a big deal. Getting the Secretary of the Navy's signature on a citation is a Big Freakin' Deal. Having the Secretary of the Navy's signature turn out to be unauthorized... is PRICELESS.
To add to the mystery: Why forge (or unauthorizedly autopen) the SecDef's signature, when numerous lower ranks could have performed this purportedly routine (but actually rather unusual) act?
This is truly something that makes you go "Hmmmmmmm..."