This was a good idea and has led me to get clear on what is going on. I think anyways
When I learn the controller using Controller Assignments in Logic, it associates the incoming midi channel number with the message, like this:
So when I turn off the output MIDI aftertouch and pitchbend, I can capture the Y movement (in this case CC # 74, and yes you can assign any CC # to this axis), but as you see, it shows it coming from midi channel 1. In the Linnstrument, when you use full 3-dimensional (Channel Per Note as its called on the Linnstrument), it rotates the midi channel per finger touch so you end up sending the CC# out through different channels. I *think* this may be causing Logic to not see the modulation from the controller in this polyphonic mode. If I switch the Linnstrument to One Channel mode, it works. When I use Channel Per Note mode, it doesn't.
In this example, it works like I would expect:
I can assign Ctrl A to CC#74, then the pitch of oscillator 1 to Ctrl A. So this is a direct assignment instead of using the Learn function.
So, how do I do this in Alchemy? In Alchemy, I can learn the controller, but I am forced to use one channel mode and lose the polyphonic capability of the Linnstrument.
I wish there was a way to simply assign a CC# to any synth parameter directly for any incoming channel and bypass the learn function and the middle man Ctrl assignments in some of Logic's synths like in the example above. Maybe there is, but I don't know how...
Hope I haven't overexplained...