I have only read the first part before Part II. Transubstantiation. The resistance to finding truth in Thomistic theology seems the clear emphasis even before reading part two. Contemporary physics both appropriates the linear model with time consistent with coherent light. That is, energy, matter and time constructed as one holistic causal group. Where folding time has specific physical qualities far apart from the biblical time of virtue and salvation history.
I expect a further reference to the chaos and randomness of quantum principles is qualified later in this paper, also. More likely in the clear but implicit manner that Father is so adept at developing. I believe this “crafting” of words unfolds more from his contemplative life than from his formal training in physics. Take that to mean a gift of The Holy Spirit.
Time in physics since duality and moreso in relativity physics has no sacred nature, is not a fluid separable from the bodies in the universe. Saint Thomas did not have these tools of modernity with which to build up. Personally, I find his philosophy and insights the more amazing and profound in how consistent and truthful his work when these physical principles were unknown. It seems to point to The Gospel expressing how the learned of this world are shown foolish by the lowly of the kingdom. Pride goes before the fall as Proverbs reminds us. Father must have worked to keep this such an academic paper when the reality of what the closed perspective of modern physics implies is such fodder for mockery and the calumny that follows.
Hope this is helpful and not too far from Father’s goal.