What we say happens to the bread has nothing whatsoever to do with the "composition" of it. The composition is what we would call an "accident", and the accidents, as a rule, remain unchanged.
I'm not saying this to persuade you or to justify our beliefs. But if you want to attack our beliefs it might help to know what they are.
When the doctrine of Transubstantiation was being developed, modern chemistry wasn't ever dreamed of. When modern Chemistry did arise (and interestingly, around the time that "subjective" and "objective" swapped meanings) the meaning of "substance" changed in popular and some technical language.
Do you enjoy or like C.S. Lewis? You may remember that in The Voyage of the Dawn Treader they meet a star on the last haven before they reach as far east as they can sail. Eustace says (quoting from memory here) "But in our world a star is a ball of flaming gas." The star replies, "Even in your world, that is not what a star is, but what it is made of."
That is a beginning of the question of substance in the old sense of what it IS, and in the new sense of what it is MADE OF.
Again, I'm not trying to persuade or anything, just trying to clarify. In general I would say that understanding our Eucharistic theology is VERY challenging indeed. Think of all the things we say about the presence of God and of Jesus. One might almost ask whether and why one might want to CONFINE the "Real Presence" of Our Lord to the Sacrament. Sometimes that seems as remarkable to me as asserting He is present there. Where is He NOT present. (No fair answering, "among you Catholics ....")
If what you say is true of catholic beliefs, then where is that supported in the Bible? It’s not, and that’s where church teachings contradict or “supercede” what’s in the scriptures. The problem is, the Bible can’t be superceded, changed, take away from. Jesus pronounces a curse upon anyone who does.