To generate the same PDF page sizes as in the Publisher document, you have to set the Print Page Size in Publisher to match the Page Size in the Publisher document.
To set the Print Page Size in Publisher:
Publisher 2003: menu File -> Page Setup... -> Printer and Paper -> Paper -> Size
Publisher 2007: menu File -> Print Setup... -> Publication and Paper Settings -> Paper -> Size
Publisher 2010: menu File -> Print -> Settings -> Pages: select "One page per sheet" instead of "Tiled" (if not already selected) or set Paper Size to document Page Size
If in the same session the user sets the paper size twice (for instance for two opened documents) it must happen that Publisher will print the second document using first document's paper size.
If you are converting a document with page size different than paper size, hyperlinks may have incorrect positions. Set the Print Page size the same as the document page size to get correct positions for hyperlinks.
The document information is imported in the PDF document only if the Publisher document is saved on disk. Save the document before converting it to PDF (Author, Subject, Company, Category, Keywords, Comments).
Cross-reference links la Publisher
Bookmarks Bookmarks functionality is available starting with Publisher 2007.
Publisher 2000 does not support Addins.