Heres a step by step for you. I have rotated Emulation Station on my machine without issue following these steps.
1.SSH into your machine (I'm assuming you now how to do this, let me know if you want more info)
Copy\Paste or Type each of the following commands and press enter
cp /etc/X11/xinit/xinitrc ~/.xinitrc
This makes a copy of like the master file and creates an editable user file
The wiki uses "Vi" to edit file, I prefer "Nano" so I have changed it for my ease of writing this.
The .xinitrc should now be displayed in Nano, Scroll down using the down arrow until you get to the following section:
# rotate the screen
# xrandr -o left
# xrandr -o right
# xrandr -o inverted
Delete the "#" in front of which way you want it to rotate.
Press "Ctrl X" , press "y" to agree and "enter" to proceed.
Should be now back at the commandline, type "reboot" to restart your machine.
The purple Bactocera splash screen does not seem to rotate. But the next loading screen and emulation station will be rotated.