As far as I can tell, if I try to make sense of this "theory" - and it's more an hypothesis, than anything...
But at the time of dealing with the Prothean VI, Shepard would not have been indoctrinated. This idea supposes that the attack by Harbinger, where the screen goes white-light at the attack on the Conduit, is where Shepard is attacked by indoctrination, while he/she is unconscious. But in the best Destroy ending, it also supposes he/she wakes up in London rubble - so what was the point of the dream sequence? This is pretty much where the hypothesis falls apart, because there's no narrative point to it. Structurally, it does not work.
And as you pointed out with the Stargazer scene - why is it present for all endings? Obviously, if this were a false ending and an "ending DLC" were to come, all choices would have to be accounted for, but again, what's th point if it's just a dream sequence? If post-whitelight doesn't actually happen, and something does in fact come after as the Stargazer scene seems to imply, and it's Shepard-centric, then nothing but the good Destroy ending can occur, barring some type of explanation - other choices result in some type of boost to the Reapers, via Shepard's subconscious failure.
It's all just speculation, though. The ending as is works on its own, and I'm not sold the destruction in that scene is actually anything in London, but I suppose it could be. I can see some of the reasoning behind the indoctrination ideas, but as they are I think they're pretty weak. But it's the internet, so it's touted as genius.
