Bread and wine.
We cannot comprehend it philosophically and/or scientifically, it is a miracle. I think that all we can really say about Christ’s substance is that the nature or essence of Christ in his glorified body is there but so also are his accidents ( according to Thomas). But his accidents are hidden behind the appearances of bread and wine which through a miracle at every consecration, adhere in nothing, being made to appear only by the power of God.
It means that the body of Christ and the Blood of Christ are really present ( i.e. and thus the whole Christ - body, blood, soul, and Divinity are present in the bread and in the wine.)
But it is the glorified body of Christ that is present. His glorified body is not the same as it existed on earth before his Resurrection. In fact the doctrine does not use the terms matter and physical. Yet, before the Resurrection we can assert with confidence that his body and blood were real matter and really physical in the earthly and scientific sense. But we know that, while his glorified body is matter and physical, it is matter and physical in a sense we cannot comprehend. Certainly a body that can pass through doors and that can consume food but not require it, and move from place to place instantaneously is something quite different. Yet, Christ calls it real flesh, flesh we must consume. More than that we cannot assert.
Yes. Post #12 answers this nicely
Be careful about attributing definitions used in philosophy or science to the same terms in Doctrine. In the doctrine of Transubstantion the term " substance " is used but not defined. We cannot assume automatically that it means the same thing as it means in Thomism ( in fact he used the term in at least two ways). Yet Thomas said that all the accidents of Christ is present, including the arrangement of the parts of his body and his dimensions, etc. But the Church does not go so far, saying only that the whole Christ is present in his glorified body.
We are talking about a miracle after all. And indeed it does lend credence to the doctrine of the Real Presence.