I took a longer look at their build/install system, and it doesn't look like it is very flexible in using external packages. It fully provides http://www.sagemath.org/packages/standard/ by default. These packages are optional http://www.sagemath.org/packages/optional/ which you would have to install after installing sage-mathematics afaik. Also, another optional package is in http://www.sagemath.org/sagedb/ which is basically a database that's worth a 2.6GB download :/ I have contacted upstream in case there is a relatively sane way of using external packages that come with the distro. I will post back if upstream says it's possible, but it looks like it won't be possible.
Mandriva has had a sage package built with external apps for a while which works quite well [1], it could be interesting to see if their spec file can be translated to a PKGBUILD. Also gentoo has a split ebuild here [2]. See also [3] for the Fedora plans for a package, although it seems stalled at the moment. [1] http://svn.mandriva.com/cgi- bin/viewvc.cgi/packages/cooker/sagemath/current/SPECS/sagemath.spec?view=co [2] http://github.com/cschwan/sage-on-gentoo [3] http://fedoraproject.org/wiki/SIGs/SciTech/SAGE