It definitely is in addition to the normal one (which really isn't that great). That's what it means that it's a boost rather than a change. I probably should make it explicit, though.
Of course, he's not just a hunter; a large part of the miscellaneous boosts was in order to let him take the sniper/guerilla role better as well.If this is supposed to replace Favored Enemy, fine. But keep the stacking bonus to Survival checks made to track that enemy. The ranger needs that ability in order to make his role as a specialist hunter viable.