Hi there. Support for NRaas mods is generally provided at NRaas. It's kind of what we are there for. :)
But the answer is that Register's Animal Control is a little bit broken right now. Some stray animals, including horses, will still spawn when set to 0. Usually we find that they don't hang around the world for very long and not usually long enough to get stuck or get into trouble as eventually the mod "notices" and hibernates them. I don't think there is any way to improve upon the 0 setting until a future version of Register fixes this.