Have a look at the new installer, it comes bundled with a modularized kernel.http://www.plugcomputer.org/plugwiki/index.php/SheevaPlug_Installer
The new installer and mainstream kernel may ease some of the challenges people face testing stuff. It will certainly make things like NFS4, USB hardware and other items not compiled into the marvel kernel easier to work with.
I still don't see any reason why you couldn't package up file-system tar-balls, but apt is pretty efficient. I suspect many of the challenges are related to customizing the kernel for specific situations rather than challenges customizing the file system.