Overlay tools are ment for DPS output only, PDFs don't support them. You actually can't embedd youTube streams to your PDF with InDesign...
SWF Preview is not very reliable for ckecking interactive features for PDF output, it's ok if you export your document as SWF. There's actually no precice PDF preview in InDesign at all...
On the other hand I wouldn't use PDF files for interactive documents at all because mobile devices have such a poor support for them.