As you correctly said, "Save As PDF" is used to create handouts or static content. There is no interactivity to the PDF content then.
Whereas if you publish from Presenter to PDF, we publish to SWF and embed the SWF inside PDF. Thus all the interactivity is maintained.
There are no specific limitations to PDF publish. All the resources like audio, video etc are embedded inside PDF and hence available when played in PDF file.
Adobe Presenter Engg. Team.
The attachments function will not work in PDF, and reporting is limited to just showing that someone accessed the PDF (no quiz interactions will be reported). Otherwise the PDF is a single page document that plays the Presenter Presentation within it
If they are just looking to have a local playback version of the Presentation, then this is a great solution. Just tell them to press Ctrl+L to have the presentation go full screen.
You are correct. It does appear that most features work. However, I haven't been able to get the attachment feature to work in the .pdf publish. Could you check into this? For some reason, in the publish as .pdf option any attachments do not appear. At least I'm not seeing the paperclip icon.
The attachments function will not work in PDF.
You can look to use the portfolio feature of Acrobat to bind multiple files together.