Philosophy was thought to be the understanding of fundamental truths more real than reality, but a lot of it was simply developing constructs that help us understand the world and survive. Even if we find a theory of everything that can mathematically describe the fundamental rules of the universe and existence, that might simply be a construct we use to help us understand the actual rules. It would be the closest thing to a form that would be more real than the material world, but it might only be an image of it.
Most philosophers didn't believe that we could be machines without an immaterial soul, but as we learn more about the brain and body, the things that can't be better explained by material mechanisms dwindles. I don't know for sure that there isn't a human soul, but if it does exist, it will probably never be detectable. I don't think it should change how we decide to live, as we should live well even if there is no afterlife.
Unless we all die, science will probably discover every rule and emergent principle that can be discovered. We'll never have every specific detail and account of our surroundings, but we'll be able to infer how our observations likely came about.