If you load a project with Instrument MIDI Control on a muted channel, the control device will not send any MIDI data. Doesn't seem to be affected by Mute mode (tested using both "Off" and "Mute").
- download the attached project file
- notice the tracks MIDI 1 and MIDI 2 (sending CC 1 and CC 2)
- check out the MIDI tab
- notice that only MIDI 2 has has been sent (MIDI 1 is muted)
- Instrument MIDI Control should be synced independent of the signal mixing