I bet it's gotta do with the annoying stance of "we don't need no steenkin' packlists!" found among Debian/Ubuntu but also some other distro folks. They simply throw out all packlists before creating a DEB package, so naturally FatPacker (and a bunch of other stuff like Module::Installed) can't work.
On Gentoo I have to deal with the same policy but at least it's easy to fix yourself as everything is installed from source. On Debianish systems I'm afraid your only solution is to forego the package manager and keep your own CPAN-installed and -updated module tree.