Exclusion Zones are used to tell StrokesPlus.net to ignore certain mouse events when the cursor is within a defined area. This is useful for things like excluding the Windows Taskbar from allowing gestures to be drawn, in which an action like maximize or close could have undesirable results.
Another example would be for mouse wheel scrolling events. Having StrokesPlus.net react to every mouse wheel scroll can result in poor window scrolling performance due to the extra processing which happens for each wheel tick. But you may want to have the mouse wheel scroll perform certain tasks only when the cursor is along the edges of the screen for example. Creating an exclusion zone for the middle area of the screen allows normal scrolling to function without interference, while allowing custom automation to occur outside of that area.