That was quite a funny (?) thread...
I would bet you money that the phrase is either taken from a Chinese source or was written by a literati Japanese in classical Chinese. "Nyo" is common in classical Chinese, as is that four-character format. Therefore it is natural to use Chinese readings.
Before I went to read the thread, the phrase immediately made me think of Shaolin temple, which is the home of kung-fu and was founded by Bodhidharma who brought Zen from India, so it makes sense that it is in the Shorinji tradition. I would have translated it as "kung fu is the same thing as Zen" or something.
Basically the guy saying it is "kobushi" is wrongly extrapolating based on his mistaken understanding of how on-yomi and kun-yomi work.