If I understand you correctly you do not want to "overlay" your PDF page (as swf page) with another "image", i.e. your other swf file?
And instead embed your swf file within a PDF file and then convert that PDF file to swf pages, with the converted PDF page and your Flash file combined into one single swf page.
We tried to embed video in a PDF file and to convert it, but at least with the version of swftools we used at that time we couldn't make it work. OK, we did not spend too much time ;-)
Perhaps a newer version of swftools does a better job. Why don't you simply give it a try? And let us know what you found out? would be a nice thing, if a complex PDF with embedded multimedia could be converted. Different content can be combined with MegaZine3, though, so it is not absolutely necessary. But would simplify the workflow.