Lockes biological passport discrepancies are not public so saying well he's had glandular fever and linking that to PED abuse (a tenuous link) is pretty weak speculation but was phrased strongly. Thats not to say its not an issue but not acknowledging the other side of the argument is ****. With less than a minutes worth of effort you can find a reasonable causal link between elite athletics and glandular fever but that takes effort and burning calories from the neck up.
Sure but that original article is about more sustained low cortisol levels which is not quite the same as the article you've linked to, which talked about lymphocyte cycles over much shorter periods, as you would expect. Clearly the low cortisol levels were on the unexpected scale.
However you're right, it's speculation at this point what the irregularities are and also right that it shouldn't have come out. Personally, the article I linked to gives me more faith in Tiernan-Locke than speculation on the irregularities