How can I prevent Author-it from publishing the blank 'allowpagebreak' style in the Word document?

You cannot prevent Author-it from publishing "AllowPageBreak" paragraphs. Those paragraphs are how Author-it controls Word's pagination. If you remove them (perhaps with a macro after publishing the document), you will have to manually paginate your document each time you publish it. All other styles have "Keep With Next" turned on, so Word is forced to break at points before Headings where those AllowPageBreak paragraphs are inserted. You can add extra AllowPageBreak paragraphs yourself for better control - you'll need to define a style in Author-it which maps to that style in Word.