It's only a trope that's used often in fiction because for the most part, it's true: you can in fact be a decent person working under an organization or a leadership with less-than-ideal methods and motives. While smaller organizations can have members that have similar mindsets and ideals as the leadership, the sheer scale of something like an entire nation, let alone what looks like an alliance of multiple nations, makes such homogenous mindsets impossible since the larger an organization or government is, the larger the disconnect between the actual citizens and the leadership in terms of ideals and personalities. There's a reason outliers, rogues, dissenters, deserters, defectors, and others exist, because nations aren't hiveminds where everyone shares the same exact thoughts, feelings, emotions and logic.
Even during the Second World War, Germany as a whole wasn't a country composed entirely of mustache-twirling evil demons bent on destruction and chaos, and even in its own military you had dissenters who tried to blow Hitler up because they didn't agree with his ways. In the same way, it's not like the Allied powers didn't have their own share of horrid things done during the war. Hell, even in this day and age you can for example commend the United States Armed Forces for its incredible ability to provide humanitarian aid during natural disasters or other crises, and still talk shit about any military campaigns and operations they do that result in civilian casualties or other unsavory activities.
For a much more personal example.... consider yourself. Think about whatever unsavory things your government has done behind the shadows. Now, would you be happy if I equated you as a person as being the same as they are?
The story of VC4 centering around Squad E and the Northern Cross Campaign doesn't have to invalidate the heinous actions done by the Atlantic Federation in the first and second games, it just means that you have to treat the characters and their actions in each story as distinct actions done by different individuals in very different circles: Claude Wallace isn't the Atlantic Federation leadership, and vice versa.
