1st: The Indoctrination Theory contradicts ME3 and its DLCs.
2nd: I believe the post-credit ME3 scene appears to be the Council Chambers.
3rd: Shepard's a cyborg; cybernetically augmented organic. The eyes are inconsequental.
4rt: EMS (troop strength) is relevant in all endings. It unlocks Synthesis or does not, it unlocks Control or does not. And determines how effective the fleet is in defending the Crucible which affects the Destroy ending.
There is no actuality here, only a randomly fitted argument. The indoctrination theory is a headless blunder operating under the illusion of a factually supported idea. If you prefer; one can argue that the vision the Prothean beacon implanted in Shepard's mind on Eden Prime is ME2 and ME3.