I am not sure (of course), but I think Atwood simply thought standardizing this format was so obviously valuable that he didn't consider Gruber might not want to work with him. In retrospect it's kind of nice that it didn't happen, it really keeps everyone incentivized to keep the format simple.
In this case a few minor edge cases is really not a big deal compared to that (in my opinion).
https://blog.codinghorror.com/standard-markdown-is-now-commo...
And an interesting discussion on hn about it: https://news.ycombinator.com/item?id=4700383
Does CommonMark count?
What Gruber has done is forced the spec to be called CommonMark, but as far as everyone except Gruber is concerned CommonMark is the markdown spec.
There are flavors that predate it like GFM, and extensions, but IMHO going forward it's CommonMark + possibly your extensions or it's not really Markdown.