Having the ending they delivered as part of their master plan would require there to be a master plan to begin with.
You should read the Final Hours of Mass Effect 3. BioWare was pretty transparent about the development of the series. The series was written one game at a time with very little thought towards an overarching narrative and choices and consequences.
IT fans can cite their "evidence" all they want, meanwhile in reality you can look at statements by the developers, the disjointed story across the series, and the shitty and very BioWare way ME3 was cobbled together and realize that there is no hidden meaning and no master plan. Mass Effect is just a mediocre series whose potential was hamstrung by a lack of planning, poor leadership, and general mismanagement and the story should be taken at face value.
You say that there are hints throughout the series but it's hard to believe that BioWare was engineering this backup plan at the same time they were demonstrating their incompetence elsewhere.
Does this sound like a team that is planning ahead? All the problems with Cerberus, ME2's general failure to advance the plot, failure to deliver on choices, inconsistent characters, and so forth strongly point to them winging it as they went along.
Finally BioWare did listen to the fans, just not all of them. People requested more information on the original endings and BioWare provided that with a free DLC. As far as confirmation or denial of the IT goes, the DLC that BioWare said was the final word on the endings merely expanded upon the three ending choices. Take the hint.