I have also wanted separate output channels in duo split and I have contacted support about the issue. It seems that it was intended, but not implemented. Though, it doesn't look to be a priority. Would be really cool since the Matrixbrutes only downside to people is the lack of polyphony. Doing this can allow people to gain that polyphony with an external device, even route it to one of the filters in the MB, and be able to control each function in the sequencer while at the same time using an external module.
I use mine in a live band setting and this would be a total game changer for us. I have already done this somewhat with a midi router from analogue solutions and another midi power device, but now I have 3 midi cables and two midi boxes layering around all the time just for this purpose. Kind of a hassle! I essentially have filtered out all data below middle C to not send any note data, then route everything above middle C to another channel. This has allowed me to play pads and stuff while using my MB for patches, bass, or for the sequencer. Not ideal but it works!