Those will be ignored anyway, see how to calculate the matrix
Also, you have to use the libinput driver … even tho you might use the wacom driver for the Stylus part … But if you use the wacom driver, then this is the approach
In other cases you have to go with a config in /usr/share/X11/xorg.conf.d/99-touch_calibration.conf
for example and have for 90 degrees:
Option "TransformationMatrix" "0 -1 1 1 0 0 0 0 1"
or for 180 degrees
Option "TransformationMatrix" "-1 0 1 0 -1 1 0 0 1"
You have to see also if you rotate it clockwise or counterclockwise … in some cases that goes with the stylus too.