The HR2046 is much the same as XPT2046 or any other Touch chip. They all have the same pinout and instruction sets. You can connect Y+ and Y- pins to the physical Touch Panel whichever way you want. You could even connect to the X terminals.
Whichever way the Panel is wired, it is fixed by the physical copper traces on the pcb.
The Calibration Utility will determine the values and directions.
If you are rotating the display from Portrait to Portrait_Rev or Landscape, you swap X, Y or polarities.
You will probably use the URTouch library with your shield. Run the Calibration sketch.
David.