I think you might be misunderstanding the following: the mod matrix outputs and inputs control voltages, not audio. The control voltages modulate parameters, typically at lower frequency than audio (but you can get also really nice effects with audio frequency modulation)
While it is certainly possible to externally process the control voltage, kaoss pad might not be a good tool for it since it is designed to work with audio signals.
You can use the KP after the brute, indeed. You can also use a different source into the kp, and connect the kp out to the external audio in on the back of the minibrute to use the minibrute filter and brute factor as effects unit. You could actually route the output of the microbrute via the kp back into the external in, which creates a crazy feedback loop similar to the brute factor (start with volume down, it might get loud and unpleasant, but maybe it can create cool sounds)