As a lark I came up with something for a game like that years ago(before MGS5) and I remember a few details. The original leader of the unit would be the chief and he's an indian(feather, not dot), ultimately making the lineage chief->boss->big boss because each one builds on the other. They also used horses because [metal gear babble about horses being more versatile than vehicles and something about native american battle strategies] and that's why the boss has a horse. The Boss's CQC was an evolution of the chiefs gun+tomahawk fighting style.
The Metal Gear Solid style of code names would also come from there because of spirituality or something.
The whole idea is really just built on the name progression, I found the idea amusing and it's not crazier than regular Metal Gear lore.