I would really suggest not to follow those steps to get your controller configured – that would effectively hard code certain buttons in your main config – meaning the auto configuration which is set on by default would get overwritten.

I would suggest using the RetroPie3 beta 2 image available here. Write that to your card and boot. Then quit out of Emulation Station and run the retropie setup script.
This will let you run the controller config – very similar to this: