Yes, we need to document the rotation/size options. The screenrotate parameter should be 1 through 3 (see this commit), for your usage values 1 or 3 would have to be used.
Does rotation work without the super-resolution (with or without xrandr controlled rotation) ? What other parameters are you using for starting emulationtation ?
Run emulationstation --debug <plus your other params> and post the output on pastebin.com. Run also xrandr --verbose and post the output.