IntelliJ has supported this for over a decade also, and having used Eclipse for PHP a decade ago, I think it's very generous to say that that was actually supporting non-Java languages as an IDE, rather than just a very slow and heavyweight text editor. I'd say Eclipse's weakness for Python, PHP, etc. at that time led to how long IDE-skepticism has been a thing.

No it wasn't, you have to have IntelliJ and Clion to debug JNI, and there are no plans on the roadmap to ever do otherwise.

In fact, the JNI tooling support on Android Studio is a custom implementation done by Android team themselves.

Isn't that mostly because Android uses its own VM, not a standard Java one?