Its very interesting that indoctrination vid like. Its amazing the little clues that have been spread throughout the game. Im not sure if it mentioned this in the vid or not but after watchign the bits about hearing reaper voices in the background during cutscenes I watched the first cutscene again when you are escaping Earth and watching that kid climb into the shuttle only for the shuttle to be destroyed. If you listen to the music during this bit its quite a sad melancholy bit of music but then suddenly a loud reaper like noise cuts through the music track, this is in the actual track of music, not just in the cutscene.
After watching the video this looks like its another sign of Shephards indoctrination as he appears sad, along with the music, but then the loud reaper noise rings out as if he is trying to battle it in his mind.
Or....... I might just be reading too much into it