Of course do I expect it to work - the manual even states that Renoise will send initial MIDI control information at project load. External gear has to continue sound generation just like the internal engine. E.g. playing a long sample via the internal sound generator isn’t affected by muting, it just toggles whether it’s audible. The same control information should go to MIDI as well.
Another example: I use MIDI control automation to setup the initial and iterative state of external gear. Since I want to render this synth to a sample and use Renoise’ modulation, I’ll need to setup a note channel for recording and a sample channel for playing. Both are mutually exclusive for recording, so I have to trigger the mute state everytime I refresh the recording. If I close the session for this day and come back to it later, I have to open Renoise multiple times and switch mute states if I want to update something. Very annoying if you also switch files multiple times per day. I’d rather like to have things grouped around their associated instruments rather in multiple channels for readability alone.