Then again, the mission to Deneva was to check up why this colony had stayed quiet for a full year! Supposedly, then, it would be extremely difficult, time-consuming and unusual for anybody to travel to Deneva (despite this place having been an important commercial hub a century prior). If the Guardian is next door to this place, it could really be out in the sticks - but one wonders why it wasn't spotted back when this neighborhood was the center of attention.
Also, "Federation space" is Swiss cheese in many episodes: locations close to Earth are quite unknown to Federation science, and if they are claimed by the UFP, the claim hasn't been enforced by any physical flag-planting. The Guardian could be on Federation soil just like the Ba'ku planet is, formally annexed but never visited, and in such an inhospitable corner of space that no competing space power bothers to make a contrary claim. But the Guardian could just as well be rewriting history in self defense so that anybody arrogant enough to make a claim notices himself suddenly lacking a pedigree...
Timo Saloniemi