There's plenty disingenuous about Pages 5.0 (like it being an "upgrade") but this isn't one of them.
The OS X user interface guidelines, which all apps are supposed to follow, says that "Save as" saves the document in its native format (.pages in this case) and that there should be an "Export" command to save in alternate formats. Note that when you Export, the document remains open in its native format so any save will be to the original file. This is different than what one sees in non-conforming programs, or on Windows, where if you save to a different format the document format changes to that if it is saved again, instead of saving to the original file.
Also, if you open a document that isn't the native format (such as a Word document) it gets Imported, creating a new document. If you then do a Save it will save a new native format (.pages) file, not perform an export.
I hope that was clear.