Jesus gave us the theology of the Eucharist.  If one philosophy more than any other can elucidate the truth that underlies "change," I think it should be used to elucidate Transubstantiation.  Thomas' philosophy of "change" comes closer to the truth than anything you or I have heard of, so why not use it?  I'd be in full agreement with you if someone were to show Aristotle's or Thomas's ideas of "change" to be false, but we don't have that.  Metaphysics being the "First Philosophy," we ought to use the best of it that we have.