And if the IT didn't have a throng of ingame features that support it, I'd agree with you.
How long will you wait for confirmation that isn't coming? The best you're going to get is "every fan interpretation is valid", which is a ridiculous cop out anyway on the part of Bioware. They *should* just come out and say that your interpretation is wrong, but someone decided two years ago that saying literally anything about the ending was going to annoy some segment of the fanbase, and so it was better to be all warm and fuzzy and accept that even the most stupid theory ~~might be true if that's what you want as a fan~~.
(Because yes, it *is* a conspiracy theory to think that they've just stayed silent about a hidden meaning in the ending for two freaking years. Fans went and assumed things about the endings that were never meant to be interpreted that way. It is dramatically more likely that those things were due to incompetence, rather than being subtle. ME3 showed that they really, really do not understand or account for how fans are going to react to something.)
They had an ending planned, and that was the one we got - taken at face value. There was no indoctrination involved. There is no grand plan to add DLC or a new game that explains how Shepard was indoctrinated.
Most likely, they'll never mention it again.