These instructions are outdated, and as shantigilbert said can easily cause EmuElec versioning issues. If you use the latest EmuELEC version (4.3 or more) you can do the following:
SSH into the device.
Find and edit the file: /storage/.config/emulationstation/es_features.cfg
Any Emulator core you wish to have native resolution option: modify the features attribute of the core element of xml like so and add to the values “nativevideo”.
For example for N64 from: