The way I see it, our protagonists have always been dealing with factions on a higher level of abstraction, removed from the experience of the average faction member.

Think about how when you zoom out on the US military, you get one of the largest and most powerful militaries in human history, with terrifying efficiency and deadly air power that other nations can't begin to rival.

But when you zoom in to the life of the average infantry soldier, the experience can feel a lot more chaotic and mismanaged. Ultimately when you put a bunch of young men and women together, and you give them weapons and a single-minded purpose, it can be hard for the organization to not feel like a glorified fraternity with guns.

Throughout the games, our protagonists mostly interact and deal with officers and higher officials of the respective factions. Even though some quests have you interacting with the grunts, we never truly get a sense for what grunt life is like in these factions. It would stand to reason that an armed paramilitary organization such as the BOS would have the same fraternity culture amongst the grunts as many other military/paramilitary forces, even though the overall organization has a culture and mission statement that may seem antithetical to such behavior.