I think it must be meant to sequence other gear as well because 16 tracks is quite overkill for a 3 note paraphonic with a few mod tracks... Also, why else would pro3 have a dedicated midi output 2? I would believe this output is what you would use for connecting external gear, and the first output being dedicated for pro 3 alone using it for sysex communication etc. Maybe... Just a guess though.
Okay, these are the sequencer destinations:
1) All synth parameters (like osc 1-3, shape mod, filter frequency, etc.)
2) All 3 parameters of FX1 and FX2
3) Modulation slot amounts 1-32
4) CV Out 1-4
5) CV Trigger 1-4
6) MIDI note on/off messages for channels 1-16 (individually selectable for MIDI output 1 and 2)
7) CC1, 2, 4, 11, 13, 14, 15, 37, 57, 74, 102, 103, 104, 117, 118, 119 (individually selectable for MIDI output 1 and 2)
Tracks 1-3 are reserved for note-related functions (oscillators 1-3), tracks 4-16 can be freely assigned.
Hope that helps.