Yes, he chose to list only the intervals in the major scale. Showing the intervals in the major and minor scale at the same time would have been very confusing.
I understand now that you weren't trying to say that minor thirds were a hole in the theory he presented, but that they were a hole in the way he presented it. I took issue when I thought you were criticizing the theory itself, because what he presented is a simplified view of generally accepted foundations of harmony. I apologize for mis-characterizing your position there.
There is more that could have been said -- and it sounds like we agree on what could have been said -- but I think it's not necessary to go into all the details of the construction of scales, including temperament, just to write a blog post. Describing temperament accurately, without handwaving, requires a book.