Dear Vladimir,
After careful reading of your very interesting essay I have immediately understood why you appreciate mine. We are connected with the same ontological approach. Majority of physicists just say: shut up and calculate. The calculus is very important, but they are not at all interested in ontology. They search "how it works" instead of "what it is".
You are right, claiming: "that new dialectic breakthrough to deep ontology which will help to find the required basic "La Structure mère" is necessary for the whole system of fundamental knowledge." There is something else beyond GUH that I did not stressed in the essay. That should be interested for you. I mean many attempts to formulate axioms in physics (D. Hilbert, J. von Neumann, L. Nordheim, H. Weyl, E. Schrödinger, P. Dirac and also E. P. Wigner). All they failed. But this is not a disaster. A deductive system can consist not only of axioms but also of already established theorems! As far, theorems were reserved exclusively for mathematics. The trick is, in my opinion, that we can use a theorem in physics, but only in the case we accept the reality is fully isomorphic to the specific mathematical structures that are covered by that theorem. Following exactly that conclusion I proposed to use the geometrization conjecture, proved by Perelman (so it is the theorem in geometry). Moreover, Perelman, in his proof, used Ricci flow with surgery. Thanks to that there is no singularities in the spacetime structure!
In my short essay I present only very general sketch that delivers the initial conditions. Many mathematical details are not resolved yet, but some you can find e.g. in: Torsten Asselmeyer-Maluga, Helge Rose, On the geometrization of matter by exotic smoothness, http://arxiv.org/abs/1006.2230v6. Torsten's publications show why not many scientists want to follow that road. Especially that this is not the mainstream research that allows to get grants. My sketch seems to be simple, but the details are really complicated.
I like very much that motto on an entrance of Academy of Plato: "Let No One Ignorant of Geometry Enter Here!" And I admire Milner's project!
Best regards,
Jacek