It's just scripting, although I didn't have to do anything explicitly for that- since Bill never takes you to the Sevii Isles, there's no way to finish the side-quest there, which is required to get the National Dex.
Ha Thanks! Just doing my bit to help the community. It'll be even better next update hopefully. Once I get to a point where I think it's pretty much finished, I'll eventually add improved graphics to make a full out more challenging Fire Red.