Sounds to me like the Feds didn't take the Hunters under their control until after the Repliforce incident- before that, the Hunters were apparently some kind of quasi-civilian agency under the control of Cain Industries. Probably, at that point, someone decided or realized the Hunters needed to have a firm hand guiding them with governmental regulation.
That would make the Hunters pre-x5 state more like... hmm, not police, but a private security firm perhaps?
That's about the only explanation I can think of for the really ad-hoc organizational behavior that we see before Signas' appearance.
I still say X is basically a Lieutenant General, especially after the fall of Abel City.