For example if we could see and trace all intentional thoughts/acts before they occurred (in matter), intentionality would cease to be a property, it would be an illusion.
All things that we know of in the universe function as physical matter, and we know the brain is a physical thing with 80 billion neurons and trillions of connections. What's the simplest explanation?
1) This is an incredibly complicated physical thing that we don't understand yet (and quite naturally so, with it having an incredible number of "moving parts")
or 2) there are qualitative elements in the universe that we don't have the scientific tools to measure or analyze, even in principle
I go with #1 because that's what every fiber is telling me (although I admit I don't know, of course). And with #1 also comes reductionism. It is a physical system we just don't have the mental models to understand it.
I also want to say there could be another aspect that affects consciousness - namely the appearance of a "present now" that we experience in consciousness. This present moment is not really explained in physics but it could have something to do with how consciousness works. How I don't know but it all relates to how we model physics itself mentally.
This isn't a matter of discovering contingent facts that may or may not be the case. This is a matter of what must be true lest you fall into paradox and incoherence and undermine the possibility of science and reason themselves. For instance, doubting rationality in principle is incoherent, because it is presumably reason that you are using to make the argument, albeit poorly. Similar things can be said about arguments about the reliability of the senses. The only reason you can possibly identify when they err is because you can identify when they don't. Otherwise, how could you make the distinction?
These may seem like obviously amateurish errors to make, but they surface in various forms all over the place. Scientists untutored in philosophical analysis say things like this all the time. You'll hear absurd remarks like "The human brain evolved to survive in the universe, not to understand it" with a confidence of understanding that would make Dunning and Kruger chuckle. Who is this guy? Some kind of god exempt from the evolutionary processes that formed the brains of others? There are positions and claims that are simply nonstarters because they undermine the very basis for being able to theorize in the first place. If you take the brain to be the seat of reason, and then render its basic perceptions suspect, then where does that leave science?
We're not talking about the products of scientific processes strictly, but philosophical presuppositions that affect the interpretation of scientific results. If you assume that physical reality is devoid of qualitative properties, and possesses only quantifiable properties, then you will be led to conclusions latent in those premises. It's question begging. Science no more demonstrates this is what matter is like than the proverbial drunk looking for his keys in the dark demonstrates that his keys don't exist because they can't to be found in the well-lit area around a lamp post. What's more, you have now gotten yourself into quite the pickle: if the physical universe lacks qualities, and the brain is physical, then what the heck are all those qualities doing inside of it! Consciousness has simply been playing the role of an "X-of-the-gaps" to explain away anything that doesn't fit into the aforementioned presuppositions.
You will not find an explanation of consciousness as long as you assume a res extensa kind of matter. The most defining feature of consciousness is intentionality, and intentionality is a species of telos, so if you begin with an account of matter that excludes telos, you will never be able to explain consciousness.