Hi Jeffbart,
Actually, the M-12 and the SEM should have the same behaviour. Please let me know if that's not the case with your setup.
Now, to answer your initial question:
1. In the Mini V3 (and the same thing goes for the M-12 / SEM), the mod wheel of your MIDI controller is hard-linked to the software mod wheel. This link is NOT removable using the MIDI mapping tools.
2. In our preset files, we have to store the current value of the mod wheel parameter. This is mandatory, because a lot of those presets are relying on this parameter's current value.
3. Each parameter that is stored in a preset triggers the "mark current preset as changed" action when edited.
That's why when you move your controller's mod wheel, the current preset is marked as changed.
Now, the point #2 is not applicable for the pitch wheel. It's not necessary to store its value in our preset files since it returns to its neutral position when it's released.
That's why those two wheels don't have the same behaviour on your presets.
Please let me know if this doesn't answer your questions.
Best,
Sam