Where in the link does it say that people thought there is a physical change as opposed to a spiritual one, "The signs of bread and wine become, in a way surpassing understanding, the Body and Blood of Christ."

There is a big difference between something that cannot have an answer and a "gap". We currently do not understand consciousness, which leaves a gap for religions to postulate about souls. But it is very likely that in the future science will be able to answer to question of how consciousnesses arises in the brain. It is not an unanswerable question.