I think it requires having a specific building. I know for a fact that it's available if you have at least 1 stellarite reactor on the world.

I don't think it's that, Final Word Protocol is Delta-tech iirc, Ultra-fractured is Alpha tech, both are below stellarite/sigma tech, so i don't think it's that.

Also it's a decision for a habitable but not-yet colonized world so i don't think it supposed to need a building on it

This decision needn't building, you just launch special project (after taking decision on planet you want to transform into fracture world, of course) and wait. When the time runs out, the planet will be transformed... or not, if you changed your mind. Anyway, you can simply use Punishment bombardment on primitives instead :) It's more faster and not costly than Protocol.