with MIOS Studio you can execute MIOS functions - which means, it is possible to enable the normal MIDI merger mode by calling MIOS_MIDI_MergerSet(1) from the debug window. You have to do this for both cores (device ID 00 and 01)
Btw.: the problem with the flickering LED matrix when debouncing is enabled is fixed now (-> MIOS V1.9c)