Actually, no. It was claimed by some of Trump's staff, who were on the trip, that Trump wouldn't have said that. What we don't know is if they were actually in the room when the comments were made and, even if they were, if they were listening at the time Trump allegedly made the comments -- and most have admitted that they were not with President Trump much of the morning. All they can testify is they did not hear the comments. Some Trump supporters claimed the article was "debunked" since no one would go on the record to confirm they heard Trump -- at least until recently.
By contrast, as Chief of Staff, Kelly would have been in the room the entire morning and, since it appears he was not the source for The Atlantic, he has corroborated that the statements were made -- regardless if other staffers heard them or not.