"As to your second para, the issue is what are "fundamental aspects of reality". One does not have to agree that the only such aspects are those described by physics: what abut mathematics for example? Or logic?"
How we define "fundamental" determines how we interpret data and build models.
While in mathematics one can arbitrarily chose any consistent set of axioms as a basis of an axiomatic system, the axioms in a physics theory should represent fundamental aspects of reality. This raises the essential question: What constitutes a fundamental aspect of reality?
What I am exploring (which I briefly discuss in my essay and at length in another work) is the idea that reality obeys a principle of strict causality. From the principle of strict causality, it follows that an aspect of reality is fundamental if it is absolutely invariable. That is, regardless of interactions or transformations it is subjected to, a fundamental aspect of reality remains unaffected.
Reality, I suggest, can be thought as an axiomatic system in which fundamental aspects correspond to axioms and non-fundamental aspects correspond to theorems.
The empirical method is essentially a method by which we try to deduce the axiom set of reality, the fundamental components and forces, from theorems (non-fundamental interactions). There lies the problem. Even though reality is a complete and consistent system, the laws extracted from observations at different scales of reality and which form the basis of physics theories do not together form a complete and consistent axiomatic system.
The predictions of current theories may agree with observations at the scale from which their premises were extracted, but they fail, often catastrophically, when it comes to making predictions at different scales of reality.
This may indicate that current theories are not axiomatic in the sense I described above; that is, they are not based on true physical axioms, that is; the founding propositions of the theories do not correspond to fundamental aspects of reality (as per the above definition of "fundamental.") If they were, then the axioms of distinct theories could be merged into consistent axiomatic sets. There would be no incompatibilities.
Also, if theories were axiomatic systems in the way we describe here, their axioms, would be similar or complimentary. True axioms can never be in contradiction.
This raises important questions in regards to the empirical method and its ability to extract true axioms from theorems it deduces from observations. Even theories which are based on the observations of phenomena at the microscopic scale have failed to produce true axioms (if they had, they would explain interactions at larger scales as well). The reason may be that everything we hold as fundamental, the particles, the forces, etc, are not. So we ended up with theorems which can be applied successfully to the scale they were extracted from, but not to others scales.
Also, theories founded on theorems rather than axioms cannot be unified. That suggests that the grand unification of the reigning theories which has been the dream of generation of physicists may be mathematically impossible because their axiom sets are incompatible or mutually exclusive.
So, what I find interesting is that our approaches are in diametrically opposed. While you propose a top-down model of causality and the representations that models it, which I see as deconstructive approach ( gathering observational and experimental data and mathematically processing it in an attempt to extract or deduce from it the fundamental laws of the Universe), I propose a bottom-up approach where were physical emerge from the smallest and simplest possible axiom set. An axiomatic approach, as I define it, is the opposite of an empirical method. I suspect that there may be limit to heuristics, a limit to the empirical method and when this limit is attained, physics may have to rely on an axiomatic approach. The exploration of top-down causality may actually help find the "heuristical" limit, if such limit exists. That limit is the point at which reality is unobservable and somewhere beyond would be the true fundamental scale.
But that fundamental reality is unobservable does not imply we can't design a physics theory that describes it. It may very well be possible to devise a complete and consistent set of axioms to which interactions at all scales of reality can be reduced to. This means that even if the fundamental scale of reality remains unobservable, an axiomatic theory would make precise predictions at scales that are.