I’m not sure if we were talking about the same:

What you hear on the MD is processed sound on the mains, synthesis plus modulation, i.e. p-lock. On your midi-out port it appears as a midi note plus a controller stream. The note you send to OT triggers a sample but it isn’t aware of the CC-stream since it has no synthesis as the MD.

MD’s sequencer dosn’t work with midi, it uses ELEKTRON-OS.