I'm answering to this 2 years and several replays later.
BioWare "denied" the IT for marketing reasons and nothing else otherwise they would've hurt their customer base.
Now on the pertaining subject: in order to settle natural laws, science works under a very basic principle, cause and effect. If an effect can be the direct result of certain number of particular causes and not others and if such causes are not only plausible but actual and the effect still takes place after them then the law of cause and effect is applicable (logical thinking).
And there's relation of cause and effect for the IT and it has nothing to do with Harbinger, TIM, the Citadel or the Starchild but with Shepard himself. It is not necessary to reach the point of getting on the Citadel to confirm it.
Shepard was in fact being indoctrinated and it showed in his dreams prior to the end of game; in fact, the last dream on the Normandy is the definitive proof that he was being indoctrinated and that his unconscious mind was fighting it because the burning child AND BURNING SMILING SHEPARD by his side symbolised DEFEAT: stop fighting, stop suffering, stop living.
This relation of cause and effect is perfectly logical and that's why it makes sense.
I remember that during my first playthrough, the dreams seemed odd at first but later raised a huge red flag with blinding red warning colours when every single element in the dreams either visual or audible wanted Shepard to stop pushing forward and fight and I still remember vividly having said to myself in a loud voice, alone in front of the screen: "he's being indoctrinated".
What happens with Harbinger later and in the Citadel with the corpses and the Shadow Broker's Ship similarities (which also stroke me as odd) can be debatable because from that point and forwards everything gets murky but the dreams aren't.
Shepard was indeed being indoctrinated and this is the result of basic dream interpretation, which is a science in itself but in order to realize this, one must be somewhat familiar with dream imagery and (Freudian) symbolism.
Besides, it is EXTREMELY rare that in a multimedia production like ME, things like all the details that lead logically to the conclusion of Shepard's being indoctrinated are present due to sloppiness: as they created the world we see according to the their whimp, we can only see what they put in there for us to see.
Such is the rule for writing fiction and creting self-contained universes.
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