I want to do this because adjusting any of the knobs for vco's or any other setting other than main cutoff knob doesn't affect the sound in Preset mode.
All the knobs affect the sound in Preset mode. The effect of the Master Cutoff will often be very apparent, and many of the other knobs may not be. In a given patch, many knobs may not have any effect at all since some sections are usually unused.
There's not a way to copy the mod matrix via software midi center?
None as of yet. If an editor comes into existence, either by Arturia or from the community, provided the necessary protocols and documentation is released, then this might change.