I am a training to become a CWI, therefore take my answer with a grain of salt, but it seems the areas to be welded should not have the coating on, so I would assume one would create a WPS without consideration for the coating. I could be wrong, though!
Also, in order for anyone to guide you on the creation of a WPS, they would have to know other details, such as, but not limited to which code you are using!
I found the following:
“Pipe lengths (typically 12 meters) are coated in a pipe mill or coating plant,
with each end left uncoated (bare steel cutback approx. 150–200 mm on each end). These ends are then welded in the field. That weld (field joint) is then coated in the field setting.”
Via:
https://www.paint.org/article/corrosion-protection-pipeline-weld-joints/