I would like to propose a modification at batocera.conf and xinitrc to handle screen rotation using the configuration file and maybe in future even using configuration menu if we have support at the menu to manipulate the system setting variable.
at batocera.conf insert the following lines:
# System screen rotation
# Possible values are:
# right, left, inverted, normal
and at /etc/X11/xinit/xinitrc those lines:
# rotate the screen
system_rotation="`$systemsetting -command load -key system.rotation`"
xrandr -o $system_rotation
As for me that have batocera installed in a external harddrive and have a laptot and gpd win 2, it is easier to change the configuration of screen rotation.