I did the same as the lesson and gave my control circle a 90 degree rotation. and then added the limit rotation constraint to the control circle, setting the limits for x to 90 for min and max and ensuring its in Local Space and it works as it should.
But, if you really need to zero out an objects transform properties you could zero it out by selecting the object and from the header menu
Object > Apply > Rotation. (or via shortcut Ctrl + A)