IMO, the early DS9/VOY uniforms were meant to be work fatigues, but they could be worn for regular duty postings at the discretion of a commanding officer. So you'd see them worn on some ships and outposts, but not all of them. Starfleet might have ultimately decided that Starfleet personnel needed a more unified appearance at the time (after the Voyager
's disappearance) and the First Contact
uniforms may have been issued to once again give their personnel a cohesive look.