It appears Nikon’s Camera Control Pro is able to control every aspect of some of their lenses (if not all) except for the zoom function… In live view mode you can focus the lens by selecting AF-S mode then you switch back to MF and proceed with the capture via SGP. This way lens remains focused and AF is not activated during shooting. During all this, the switch on the lens remains at M/A position.
I have tested this on the following lenses
Nikon AF-S NIKKOR 14-24mm f/2.8G ED and
Nikon AF-S DX NIKKOR 35mm f/1.8G
Hope this is useful for those who are shooting with Nikon glass
Sedat