I haven't found a way to do this, so I think it's a feature request: when I'm experimenting with finding the right color palette, it'd be super helpful if I could do a global paint bucket operation, replacing all voxels of one color with another color, across all the different matrix objects in my model. Right now I have to drill in and out of a bunch of different models to try out each color change.
Related but separate feature request: I'm using Qubicle to mock up an entire scene for a grid-based game. To mock up a full scene I end up copying some matrix objects a bunch of times, like my ground tiles. I found some great tools in Qubicle to make this easier, like the "Duplicate Special" tool to more quickly make a grid, and using compounds to easily export only the "master" copy of each matrix. But one additional thing I'd love to see is a true "original master/copy" relationship, where I'm making linked clones of each matrix rather than independent copies. That way I could edit one floor tile, and all the other copies of that tile would get the same edits. This could make exporting easier as well, by only exporting one copy, the master, and not all the linked clones.