When you open a regular PDF in e.g. Reader X, you cannot save the file, you cannot load a form, partially fill it and then save it for later, you cannot add annotations to the document to participate in e.g. an online review, and a few more things that you would need Adobe Acrobat for.
When you save a PDF as Reader extended file, you add something to the file that allows Reader to run in a more powerful, feature-rich mode: All of a sudden you can modify and save the file and do a bunch of other things.
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com