The hardcopy "binder" (3 D-ring, seperation tabs, the content on the sheets of paper, etc) is not supported by anything "digital".
One can add 'stuff' on the digital file to kinda-sorta more or less simulate the hardcopy. However, such is a pale imitation of the hardcopy binder and it shows.
A PDF Portfolio provides a flash user interface.
Think of it as a PDF "wrapped" by Flash.
A Portfolio can "hold" supported file formats as well as PDF files.
These are attachments to the host, Portfolio PDF.
The flash interface provides several layouts for presenting attached content.
These layouts support various user ascribed configurations.
Pretty neat. But, because of the Flash user interface, Portfolio usage is pretty much limited to use of Adobe Reader and Acrobat.
Regarding PDF Bookmarks -
These aren't available in the Portfolio PDF (the Flash interface).
In a standard PDF Bookmarks can be created. They live in the Bookmark panel of the Navigation panel.
So, any PDF files that are attached to a Portfolio PDF can have Bookmarks.
The Flash interface displays a thumbnail view of the file. For PDFs, when you open the file the bookmarks can be viewed and used.
As always the Acrobat Help provides an informative discussion of all this.
Use the following URI to visit the Acrobat Learn & Support page.
Links to the PDF Help for Acrobat XI, X and previous versions are present.
Be well...