I suggest changing the documentation rather than the code.  The mix up is in the wording.

Documentation below
"If shallow is true, files with identical os.stat() signatures are taken to be equal. Otherwise, the contents of the files are compared."

The "Otherwise" appears to be referencing the "If shallow is true" cause, when it should be referring to the equality of the _sig()s.

Proposed Change 
"If shallow is true, files with identical os.stat() signatures are taken to be equal. If they are not equal, the contents of the files are compared."