How does scientific progress happen without reasoning about that which we do not know or understand?

That's building upon current knowledge. That is a different application.

Sure, but you (a person, not an LLM) can also reason about what you don't possess, which is one of our primary learning mechanisms - curiosity driven by lack of knowledge causing us to explore and acquire new knowledge by physical and/or mental exploration.

An LLM has no innate traits such as curiosity or boredom to trigger exploration, and anyways no online/incremental learning mechanism to benefit from it even if it did.