Do you de-hull seeds when making pumpkin seed flour?
Whether or not "you" specifically choose to de-hull pumpkin seeds before grinding them to make flour, pumpkin seed shells are certainly edible, both raw and roasted. The first source you name certainly seems to be referring to pre-shelled pumpkin seeds, not just because they mention it being green, but also because their image of finished pumpkin seed flour is comparable in color to the ground pumpkin seed flour I've made from just the kernels. 


  Note 1: It is green…so you might not want to use it for almond flour
  vanilla cake (or other such light colored dishes). I am sure even if
  you used sucanat for a sweetener in a baked good it would be enough to
  cover up the light green color.


Hulling pumpkin seeds is a chore without a hulling centrifuge, but the easiest way I've found is to roast them, chop them in a food chopper, and then separate the kernel bits from the hull bits using a bowl of water (the kernels will sink, the hulls will float). 

While pumpkin seed hulls won't damage your GI tract the way other nut hulls will, they're mostly fiber and some carbs, with a little boost of zinc in the attached endosperm. Thus, the relative difference in protein/fat/simple-carb/fiber levels will affect the texture and nutrition of your final flour product, so the choice of whether to hull or not depends primarily on whether you want this to be more of a protein powder or more of a baking flour.