since i am still waiting for my matrixbrute, i cannot say, if it is possible to run an "empty" sequencer (to drive the tb03) and play notes on the MB without recording them into its sequencer
(which is your problem, if i got this right: if you shut off the MB and the TB03 is set to external sync, then it CANNOT run)
but an easy solution would be:
make the TB03 the master (= TB03 Midi out -> Matrixbrute Midi in)
by this, you could switch of the MB sequencer and the tb03 would keep running.
to sync them again, you might have to restart the tb03 though, i guess (maybe not, check it out)
good luck