How can Big Boss command in Fox Hound?

I know more or less the whole story I think but something feels off to me. Forgive me if I assume something wrong but I'm here to ask, so I suppose I can have a proper feedback from you.

Big Boss represents a threat for Cipher, right? And so, I suppose, even for the goverments or whatsoever.

So, as he was kinda searched and hunted down by XOF and Cipher, how can he be openly commander in Fox Hound, that I get it should be an official squad for US military (or something like that)? Wouldn't he be considered kinda like a terrorist or still easy to find and put down by Cipher?