They'd be best described as "Mutant Rebels" faction, enterprising folks loosely affiliated with Mutant Alliance who protects them. Their cooperation with Govt is circumstantial and only happens if you tick them off enough to launch a Crackdown (at that point, the Alliance is strong enough for these guys to secure Govt support for a Crackdown). Normally there are no Govt units during the only mission this faction flies (so far), the "Rebel Trading". In the future, they will be also flying "Rebel Patrol" mission or something like that (a mission which has a chance to thwart a monthly Pogrom).