> it would be much better to examine the internal state and activity of a "thinking system" directly
The particular problem here is complexity management. The 'problem' with thinking is it is a system, very possibly one of the largest and most complex systems we know about. Thinking as we know it in DNA based life is something that's at least 500 million years old and developed a few bits at a time. There is no unwinding the different components of the thinking from each other. Motor skills, reactions, learning, etc are all compressed and mixed together in the same code.
So, going from top down isn't working. But going the other way isn't working either. The computational complexity of a system that gets anywhere close to a biological thinking system requires quadrillions of calculations.
These are philosophical questions that really, despite our best efforts, have never transitioned to a true science, and philosophy has been working on it for thousands of years. We've been hamstrung by the fact that as far as we knew, we were the only intelligent beings in the universe, so it's extremely difficult take any aspect of "the way we think" and separate it, by finding some system that thinks in some ways like us, but in other ways doesn't. It's really only been since we've had large neural networks that anything has approached the way we think in _any_ aspect, so this is probably a once-in-history opportunity to formalize and systematize all of this.