B-17s, Ju-88s, B-24's, and other heavy bombers generally used a tactic where tight formations and massed firepower were their defense (at least in daytime bombing, which is the only thing we have in the game). When attacked by enemy fighters, they stayed in formation. We get this in a small sense with the three plane box.
Stukas, TBMs, and SBDs all had defensive guns, but when attacked by enemy fighters, would disperse and maneuver rather than tighten up and depend on return fire for protection. As such they do not get a three plane box.
Different tactics, different methods, and not surprisingly, treated differently in the game.