Interesting point and thanks for posting. I wasn't aware that a new clean UEFI install reverted this, although it is mentioned in the guide that you should already have a full clean install of El Cap (typically) before proceeding.
As mentioned though, and as you point out, once you have the OS installed, if there are any issues getting this method to work you can simply do a bios reset and begin the UEFI fix again as if you were starting from scratch. Useful if you make a mistake or think you might not have got it quite right.
No need to re-install the OS or Clover either so long as you have done a standard install.