These emergent properties that you mention (temperature, intelligence) can in principle be described by the individual components (particles) along with the fundamental laws of physics that govern their interactions. The emergent property that we observe is just a cognitive abstraction designed to strip away the complexity and describe the aggregate behaviour of the group of individual components.

Our mind was designed to work this way. The most advantageous way to perceive a rock is as a single object with properties pertaining to utility (hardness, potential weapon, etc). This takes the least cognitive load and is the most beneficial way to perceive the world from a fitness perspective.

There's nothing epiphenomenal above and beyond the individual components (and the laws governing their interactions) except in our minds. In that specific sense, emergent properties are an invention.

I wrote an explicit example for a case where your analysis doesn’t seem to be correct, but you didn’t resolve the issue — temperature makes new observations possible that were not possible before and it is not tied to the human reasoning (also, it is only but one example, perhaps not even the best).

I don't know if the assertion you made is true, ie that an omniscient entity can't explain everything there is to know about temperature by looking at the simple movement of atoms. What's the basis for this? I know you followed that up with a rationale, but I didn't really follow. Just because this abstraction (temperature) allows us to come to conclusions and inferences about state and state changes doesn't mean that there's anything real about the abstraction aside from the cognitive structure in our brains that helps us to process the world around us effectively.