My disagreement with this paragraph was with the implication that "these supposed inconsistencies were [intended as] dispositive proof of the paper’s secret age

My disagreement with this paragraph was with the implication that "these supposed inconsistencies were [intended as] dispositive proof of the paper’s secret agenda", as opposed to the more obvious accusation that there simply was no hard and fast real name policy: perhaps the reporter was mistaken that there were no exceptions allowed, or was not willing to make the case to his editor that anonymity was justified, or had already made the case and had explicitly been denied. Only the last two of these might fall under "secret agenda", and even then it's still more likely to be the opinion of one editor or one reporter than the agenda of the paper as a whole.