I made a script for rendering a Multi Matte output. You can download it here: http://j.mp/23hAN4B. It's not quite as slick as having a proper render output, but it'll do in a pinch. You should put the whole MultiMatte file into your kits directory. If you don't know where that is, go to the Scripting layout and use the Open Folder menu at the top of the screen. If you're on 901 or above, you'll be able to call up the GUI with mm.gui. Hope it helps you!