Yes, I think we agree. 
I don’t think you are saying otherwise. But I read it as almost implicit in the idea that physics could somehow disprove emptiness with its methodology. If we accept that premise, then it says something about how someone would or could arrive at knowing emptiness. And I think that if we follow that to its logical conclusions, we get some problems.
Here is another way of framing what I am talking about:
I think that when the Teacher spoke of emptiness, he was generally speaking of the emptiness of sense experience. By emptiness of sense experience, I think that he was claiming that sense experience arises dependent on other things, and that it is impermanent. I believe that he claimed these were empirical observations that he had made which had psychological and philosophical implications.
Say we are investigating an instance of matter—say, a pebble. We could call that pebble a “basis of consciousness.” Meaning it is the basis for the arising of sense consciousness at the various sense doors, without which there would be a shift in conditions and a ceasing of that corresponding consciousness. There, we can refer to a dependent structure for the arising of experience, as well as impermanence.
No experience of pebble → Conditions shift → Conditions arise where the pebble is a condition for the arising of eye consciousness dependent on functioning faculty of vision → Sense contact with the experience of a pebble → Conditions shift → No sense contact with the experience of the pebble.
Suppose that during this process, the perceiver decides to investigate the matter of the pebble. Trying to reduce it to fundamental components that may be present in the pebble. In this case, they are investigating the basis of consciousness.
While I think it is interesting and not unrelated to find that there might not be a kind of irreducible particle or wave or something in the pebble, it really has no bearing on the fact that every instance of investigation itself involves the arising and ceasing and shifting of dependent conditions for more consciousness to arise with different bases and impermanent events. No matter what they found there, it would really have no bearing on that structure of consciousness and its arising. Because in order to even do the investigation in the first place, this kind of structure had to be operational in this way. No ontological assumptions should be made about a kind of external substance based on the investigation either, even if they did seem to find an irreducible particle. Such ontological assumptions would be unwarranted. There are a series of other things, such as proving its eternality, that would be needed to approach it being a fundamental essence, I’d say.
Moreover, variety in the quality and persistence of sense faculties can be clearly observed. Some people lose their vision. Sometimes vision is inoperative. Sometimes the qualtiy of vision changes, diminishes, etc. Similarly with the other senses. So despite the basis of particular conscious experience, the faculties that the consciousness is dependent clearly do change. Of course, I am speaking conventionally here, not of some kind of faculty or consciousness thing which has the property of change.
I agree those and likely others are all reasonable possibilities This is a mere example of one of the questions that I think should be addressed if someone were to seriously relate Buddhism to Physics beyond the level of curiosity. Because it doesn’t take a genius to observe the stars and see that the movement of the sun and moon cannot be because they move behind one side of a large mountain at the center of a flat earth, as some Buddhsit texts claim (though I don’t know if this is stated directly in any āgama texts).
(Aside for what it’s worth: I think the descriptions of Mt. Meru and so on are meaningful, and I don’t think the only meaningful way to relate to cosmology is in terms of sheer observational accuracy for humans. Also, it may not take a genius, but I am not a non-genius enough to know how astronomy works to even disprove that the Sun moves behind a mountain! 
)
All the best!
