That egg was totally still edible, even if you pierce it for the cooking, it should be good for at least a few days. If you do it right, it can be weeks.
In Germany you can buy cooked eggs in the super market and they are not refrigerated.
This article was weird, in that he went through the whole thing about how effective the layers are without also mentioning there was a hole through all of them other than the egg white (until the end).
If the egg had bacteria already growing in it (which is also unlikely) then it's possible that enough of the bacterial toxins could accumulate and be inside when you eat it.
There are probably a number of extremely rare scenarios which would modify the situation but this article includes a lot of words and facts only to come to the unlikely conclusion.