I re-read your post, and it can actually be summarized by one central consequence of the MCogito logic: Thought knows only Thought; ideas know only other ideas.
Consequently, Materialism knows only the idea of Matter. Materialism is merely a low-fidelity (low-Q) version of Plato’s idealism: the idea of Matter has simply replaced Plato’s idea of the Absolute.
The immediate objection naturally arises: “But we know physics is real! So how do we know it?”
This question is strictly impossible to solve within the defective [Nature-Human] bi-categorical framework of classical Philosophy.
It leads directly to the circular aporias you described: materialistic reductionism still needs to be conceived using the categories of Thought (equality, logic, etc.); therefore, it has no truly independent existence from Thought.
All of these aporias vanish instantly within the [Matter-Life-Thought] multi-categorical framework. In this system, the Thought category is totally independent of Matter, yet it knows Matter intimately via the metaphysical concept of the “differential speed of Being output.” as you can (but will not) discover here : A new concept of causality for the matter-life-thought multi-categorical metaphysics