There is an additional set of margins in a Pages document.
I exported a document to Pages '09 and opened it with the old version. In the Layout Inspector, I found the "Layout Margins". The "Left" and "Before" margins were non-zero and the numbers matched the unwanted margins I saw in Pages 5.2. Here's a sample:
I changed those layout margins to 0, saved the Pages '09 document, and opened it in Pages 5.2. Hurrah! The unwanted margins are gone!
If there's a UI control to view or change the Layout Margins in Pages 5.2, I haven't found it.