But, there's reason to doubt they will, as this was never their intention with the ending. Yes, the video pieces together compelling evidence. Yes, it's a very strong desire on our parts to explain away how unfulfilling and disjointed this ending felt compared to the rest of the Mass Effect experience up to that point.
I'm going to push past much of the evidence offered in the video. I will say that visions of a child throughout Shepard's game doesn't exactly mean his final experience was entirely a dream. As he saw the child outside of dream-states (such as on Earth prior to escaping), it stands to reason the ending sequence may not have been intended as a mental vision. It could just mean they were trying very hard to be very poignant by including the vision of a child in a very harsh and dark setting. It's sometimes what writers do.
A lot has been made of Bioware's writing. A little too much. They're good at interpersonal motivations and dialog, but their grand-scheme writing actually reverts to using a lot of cliches (outer space "warrior" races, evil mega-corporations, evil mercs, a race of all-female human-enough-looking space hotties who can reproduce with anything, etc...). It could very well be that the writers are fantastic at putting together stories and settings that people find compelling, but they just suck at wrapping it all up in a concise ending that deals with all the loose ends. Some writers just suck at endings. I'm not excusing it. After ME2's fairly fantastic ending sequence known as the "Suicide Mission" which was very gratifying, there is no excuse for ME3's ending. However, these things happen, especially as creative types get so wrapped up in trying to convey an artistic message and lose sight of the emotional expectations of the fans of, what is essentially, an interactive and customizable fiction.
In order to buy the Indoctrination Theory regarding ME3's ending, we have to assume some things that I'm not ready to. We have to assume that this was Bioware's intent: a MASSIVE open plot-twist, the nature of which is not revealed in the actual game purchased by millions of fans. The evidence for this monumental twist is subtle enough to require most of them to figure it out by going to YouTube and seeing video analysis put together by commentators with that much time on their hands. If they had this twist in mind, why would they rely on THIS method of revealing it? If they did, they missed the opportunity to knock a plot point out of the park, and leave their fans salivating for more. I can't believe they would... I can't believe it anymore than I could believe the writer of Fight Club would decide to NOT make it clear (eventually) that the narrator had been Tyler Durden all along. Bioware would have realized that this reveal would have been a defining moment in the game, a literary home-run that would cause all the "what?" moments to finally snap into crystal clarity and really wow their fans. In order for the Indoctrination Theory to hold water, Bioware would have had to have made the conscious decision to NOT include this reveal, and intentionally leave most of their fans confused and disappointed.
If they do adopt the Indoctrination Theory for the end of this trilogy, I would have to assume it was because those hard working video analyzers and hopeful fans gave them the idea afterwards. Because of the prior paragraph, I can't believe it would be intentional prior to the release of the game.
There's also too much extraneous video footage in the ending sequence. If their intent was to "restart" galactic civilization (as the ending obviously declares) the sequence where the Normandy is fleeing battle and crash-lands makes perfect sense. Despite the plot-hole where the squad-mates who assisted in your final battles are on the Normandy - I would state that the squad-mates depicted are simply the ones the game knows for a fact survived, and that would be the ones you picked for your final missions. I think it was a decision that made programming easier. If it were a "vision", it wouldn't fit in. Why would Shepard be having a "vision" of the Normandy fleeing the field of battle and crashing? Why would this vision go unexplained? Why would they offer it as canon on the surface to their fans, without any clarification until the fans demanded one?
Equally damning is the video at the end of the credits, where it's obvious that galactic civilization has reset to a pre-FTL state. It puts the final cap on the Mass Effect universe and slaps the label on it signifying a "finished" product. Any future DLC, stories, games, whatever, that take place after the ending of ME3, have to contend with that after-credits video. I'm not saying they can't remove it from the game, just like Valve changed the game-ending video to Portal when they realized they wanted to make a sequel. What I'm saying is it wasn't their intention to do so when they created the game and proclaimed it "done". The only thing that gives me some heart about this incredibly finalizing video is the reference to more Shepard stories. It could be just a literary line that sounds intriguing but ultimately means nothing. If there is more Shepard to be played, it would contradict all the claims that ME3 would be the conclusion to the Shepard story, which I still think was Bioware's initial intent, regardless of whether they change their minds after this.
Supposedly the DLC that "clarifies" and expands the ending is coming out this summer, and it'll be free.