According to Merriam-Webster, the masthead is also "the name of a publication (as a newspaper) displayed on the top of the first page."
This article seems to be referring mostly to the masthead in website applications and layout.
However, I've been with a newspaper for nearly 20 years, and I can definitively say that what we call the masthead is the name of the newspaper at the top of the front page.
We call the box with the information about the publisher, etc., the "publisher's box," but this may not be true at every newspaper. That's just what we call it.