To the best of my lay knowledge, these are not synonymous terms.

Here's a recent professional journal article on the subject: Atypical depression: current perspectives, authors Dorota Łojko and Janusz K Rybakowski
From this I understand both families of disorders, depression and bipolar, can be sub-categorized in atypical forms.

Of course, that doesn't mean laypersons and even professionals won't use the term any way they want. You'll have to ask whoever is using "atypical depression."