As far as I can tell the script /usr/bin/mkdesktophdicons creates the desktop icons on bootup. I don't know how it is getting called, although I have a feeling it is getting called from the /etc/X11/xessions.d/45xsession file. You might be able to edit the /usr/bin/mkdesktophdicons script so that it creates the icons in a folder.
I hope I am right and I hope this helps.
James