Yes, Chris. The idea being if your were, for instance, in a Top (plan) view, and some of the your model structures were on the diagonal, you'd change the axes to match those structures in order to draw/edit them. If you wanted to zoom in on a particular area of those structures on the diagonal, the Zoom Window tool would be able to drag a bounding box relative current axes to define the zoom window.
Otherwise, your forced to right-click on the user-defined axis, pick align view and then use the Zoom Window tool.