at the beginning, I experienced the same issue with both the touch and the pen, when upgraded to ScreenpadXpert 3, the touch worked as expected, but the pen remained the same, finally, the ASUSScreenPad2Optimizer fixed them (it seems it's setting some flags that doesn't have a user controllable settings).
Actually, it would be nice if we can switch between the two behavior, especially for the pen, it's sometimes nice to use the pad as tablet for the main display