TP is not suited for statistical analysis and Xact TP for a cylinder will always report 'WORST END' (legacy gives you a choice, ASME/ISO/Xact doesn't), which will complicate the matter even more, as you have seen. If you need X and Y values, why don't you dimension X and Y values? Or at least do a TP on top and bottom circle separately?
TP is not suited for statistical analysis and Xact TP for a cylinder will always report 'WORST END' (legacy gives you a choice, ASME/ISO/Xact doesn't), which will complicate the matter even more, as you have seen. If you need X and Y values, why don't you dimension X and Y values? Or at least do a TP on top and bottom circle separately?