9. Same issue for the Neutrality Learning Center and the Research Academy (for example), though this is a bit of a different case. However, shouldn't the latter automatically upgrade to the former?
Nope. The NLC is a completely different line of tech. It is a class by itself. That is why both lines are still present to build after it is researched.
The Research Acadamies will upgrade to the Invention Matrix then to the Discovery Sphere, but as far as I know that is as far as they go in that branch.
The NLC is one of the first techs I go for since it has the highest research value (22) of any of them, and is cheaper also. Once those start going in the research goes incredibly fast.