Hey Jason, this is actually possible to do and it is fairly easy ... apparently. There is a thread in the forum about it somewhere but I can't find it now. I have been asking this question a few times but I haven't try it myself yet. And I am sorry I don't have time to try it now but here is what you should have to do...
When you finished with the tour you just need to create a few different outputs with different starting points. So lets say you have a tour with four panos. Firstly in FFC set initial pano to 'pano1' with custom initial possition and flashificate into folder 'tour1'. Then change initial pano to 'pano2' and flashificate to folder 'tour2', etc. etc. So you end up with four tours (folders) where each one starts from different pano. But all the tours use same visual files, same hotspot files, same plugins, etc. So really the only two files which change are index.html and xml file.
Next you need to put four folders into one which means just keep html and xml files from other folders and put everything into one. Lets keep first folder (tour1) as a main one. Open tour1 folder and rename index.html to tour1.html. Then open tour2 folder and rename index.html to tour2.html. Then copy tour2.html to tour1 folder and also copy tour2.xml to tour1/files/xml folder. Now you can delete tour2 folder. Do the same for other folders and you should end up with one folder named tour1 where you could see tour1.html - tour4.html and in xml folder there should be tour1.xml - tour4.xml.
So now you just point to particular html file according to the panorama you need to start from.
I hope it help. Please let us know if it work out for you!