He's driving Quartz Composer via MIDI, which for what he needs is quite satisfactory for now. You'll notice that in the newest unstable releases EigenD now creates it's own virtual MIDI in and out busses on the Mac - this was implemented to support closer integration with Quartz Composer without needing to set up an IAC bus, which is hard to do in an installer. It has the nice side effect of making wider MIDI interoperability that bit easier as well.
And I agree, you really need to see Stuart's stuff live. I had a play with one of his patches, projected on a screen in a dark room, and it was amazingly compelling. One could waste quite a bit of life just noodling about with it...
John