Rob has mentioned in other posts that you are able to adjust the default values of an analysis such as VSPAERO by saving the vsp3 model with the values as desired. You could set the Sref in the model, save, and then run a sweep of Mach numbers. Or you could try setting the value with SetParmVal() using the WaveDragSettings container, Sref parm, and WaveDrag group. If you can't directly obtain the container for the wave drag settings try the snippet of code below written in AngelScript.
void main()
{
string wds_id = FindContainer( "WaveDragSettings", 0);
SetParmVal(wds_id, "Sref", "WaveDrag", 100.0);
Update();
}