I find it difficult to accept the idea that capable, creative, and critically-thinking professionals could have purposefully constructed the nonsensical ending to Mass Effect 3, as it currently exists.
Instead, I believe that Bioware did indeed set out to create a coherent, satisfying, and internally-consistent ending to Mass Effect 3, as promised. However, those ambitions were ultimately derailed by time constraints and a lack of clear creative direction.
I suspect that at some point during the production process a critical deadline was reached, and it came down to the ending simply not being ready to go at that point in time. Unable or unwilling to delay the game any longer, the game's producers made the decision to salvage what they could from the ending content that had theretofore been produced and, to the best of their constrained abilities, cobble together those bits and pieces into something that would at least "function" as an ending. The final cutscenes (Normandy fleeing, Giligan's planet, etc.) appear to me to be nothing more than scraps stitched together from wildly disparate sources and contexts in a desperate attempt to give the ending something resembling a conclusory trajectory.
In it's current patchwork form, I believe the ending is meant to be taken literally. I don't believe that there is any deep or profound meaning behind it at all. Nor do I subscribe to the indoctrination theory, insofar as I don't believe that indoctrination is meant to play a role in the ending as we have it now. However, I do believe that an indoctrination plotline was supposed to have played a role in whatever original ending Bioware was working towards because the leftovers of such a plotline are all too evident in the ending as it currently exists.
Moreover, I don't believe Bioware ever gave any real consideration to the implications (cataclysm of relay explosions, etc.) of the current ending. Time constraints being what they were, they simply lacked that luxury. They had a deadline. They had to have an ending. This was the best that they could do.
Simply put, the ending is a hack-job, necessitated by a combination of systemic and creative breakdowns.