Yes, it's different, but the article was trying argue that since "X" wasn't used in that context at the time it was introduced as a GUI element, the GUI element

Yes, it's different, but the article was trying argue that since "X" wasn't used in that context at the time it was introduced as a GUI element, the GUI element couldn't possibly be referencing the letter as a way of closing a program. While I agree that it's unlikely that the GUI "X" refers to a letter "X", that's not a valid argument for that position. Edit: and thanks for the vi ref.