I think that description was more confusing.
As I said,
The colours set by a shape script are only overridable if you call drawnativeshape.
As an example:
shape main
{
if(hasTag("red","true"))
SetPenColor(255,0,0);
// Will be drawn with a red border unless
// user has overridden it on the diagram
drawnativeshape();
// Will be drawn with a red border
setfixedregion(-16,0,0,16);
ellipse(-16,0,0,16);
// Will be drawn with the colour defined by
// the user for the diagram or object
SetPenColor(GetUserBorderColor());
setfixedregion(-16,16,0,32);
ellipse(-16,16,0,32);
// Will draw the border in the user defined
// fill color
SetFillColor(255,255,255);
SetPenColor(GetUserFillColor());
setfixedregion(-16,32,0,48);
ellipse(-16,32,0,48);
// Will ignore the user defined border colours
// and draw using global colours (including
// element grouping colours if applied)
SetPenColor(GetDefaultFillColor());
setfixedregion(-16,48,0,64);
ellipse(-16,48,0,64);
// Filled with status colour if set to be used
// for this element type. Otherwise element fill
// colour. Doesn't apply to pen colour
SetFillColor(GetStatusColor());
SetPenColor(GetStatusColor());
setfixedregion(-16,64,0,80);
ellipse(-16,64,0,80);
}