They weren’t kidding about the “crazy”.
Look, it’s not as if Mass Effect fans MADE UP indoctrination. The main villain of ME 1 (and his sidekick Asari chick) both succumbed, as did many other people in ME 1 and 2. Just being AROUND Reaper tech is enough to indoctrinate people. That’s why it’s so dangerous. The Illusive Man in ME3? Indoctrinated.
With all that groundwork laid, Indoctrination isn’t so much a “crazy fan theory”, but “the only explanation that makes any sense”. Just FYI.