Obviously, there was some indoctrination-like business going on during the TIM conversation but that just goes to further show the point I made above. Indoctrination is a plot device now that is used for whatever, whenever convenient. Because what does TIM actually do? He doesn't really indoctrinate Shep (Shep can still express his thoughts freely) but he controls both Shep and Anderson like puppets. What is that even? It doesn't follow the rules anymore that were established in ME1. It doesn't follow any rules at all so it's useless to speculate about it.
Puppeteering is usually a stage of indoctrination only achieve after visible physical alterations (source: ME Retribution). TIM controlled their bodies without controlling their minds. Which imo demonstrates TIM's fundamental misunderstanding of indoctrination and Control.
Apropos the dreams, here's my explanation (referring to indoctrination only, not IT):
- the dreams are an attempt at indoctrination. Basis: Mass Effect Retribution (Grayson's transformation, esp. the whispers, pp. 54-56, that get louder as the indoctrination progresses), ME2 Arrival DLC (for dreams), Rachni queen in ME1 (shadows)
- Shepard fights the indoctrination by attempting to find the source of the indoctrination.
- the indoctrination construct - i.e. Reaper influence - is manifested as the boy. This makes sense imo, since, like Leviathan's meta conversations in Shepard's head, the other entity assumes a form drawn from his /her memories. The fact that boy's image again returns manifested as the Catalyst indicates to me that the entire Catalyst conversation also happens in Shepard's head, but that's me getting side-tracked.
- The boy runs away, out of sight, hiding amongst the shadows. Twice, when Shepard gets close to finding the boy, a red light shines, the Reaper chord blares, and the boy runs away again. That could just be a flashback to the boy's death in the shuttle, or it could be signaling Reaper presence.
- Shepard hunts down and finds the source of the indoctrination, which goes up in flames when he finds it. Shepard doesn't seem to know what the dreams are (even though (s)he should, given his / her history), so still looks horrified at the sight. Or perhaps Shepard DOES know that (s)he's fighting indoctrination, but obviously can't confide that to anyone.
- Hunting the source of the indoctrination gets harder later in the game (not really harder, since there's no way to fail the section, but narratively speaking, it's harder) as the "oily shadows" grow thicker, and the whispers louder (after dosing Grayson with red sand, "he could understand the whispers perfectly." This was still relatively early in Grayson's indoctrination since no physical alterations had happened, but that would occur soon; the next stage is "[Grayson] was horrified to discover he was a prisoner in his own body" (59)).
- part of Shepard is slowly becoming indoctrinated, which is why a version of his adult self joins the boy in the third dream. But he fights / finds this source also, and again the Reaper influence is destroyed - even if destroying it means destroying himself / herself. Which to me sets up the Destroy ending with perfect irony: Destroy is chosen by Shepard with the idea of self-sacrifice, and that is actually the one ending where (s)he physically survives. (The Catalyst tells Shepard that (s)he might not survive Destroy, since (s)he is partially synthetic, but that is revealed to be BS if you've talked to EDI about transhumanism.)
- Since Shepard successfully finds and destroys the attempts at indoctrination, the Prothean VI does not detect him as an indoctrinated presence.
So, by the time TIM tries to pull that indoctrination sh*t on the Citadel, an attempt at Control that is based on misunderstood concepts, Shepard has literally been there, done that, and can shake it off.
Sorry, long post.