Reply to Volume controls different from S4

I have both the VCI-400 EGE and the S4. I've noticed pros/cons to both but overall I'd have to say I like the VCI best due to the expanded creativity I can bring to my sets.

However the volume controls bother me. Why is it that on my S4, the main volume knob controls the volume but you have a 2nd level of control within the software with the main level knob. When using the S4, I used to leave the main level within Traktor set at like -1dB and then control the volume with the faders and knob on the S4. This used to help me from clipping.

With the VCI, the main volume knob directly affects the main volume within the software so you don't have that extra level of control.

Has anyone else noticed this and is bothered by it? Anything you can do to get it to behave like the S4?