The problem you face is that transubstantiation is supposed to be a theory about what physically happens to a wafer. That said wafer is composed of molecules, atoms and, ultimately, subatomic particles. That is all there is to the physical constitution of a wafer.
No, transubstantiation very specifically says that absolutely no physical change occurs. That is why the accidents (physical properties) of bread and wine are said to remain. What’s more, transubstantiation goes even further and says that the physical properties remain without being directly connected to ANY substance; Christ’s flesh and blood do not take on the properties of bread and wine which remain.
The physical constitution of a wafer doesn’t touch on the essence of “wafer”, except indirectly in the case of “essential accidents” which I’ll explain below.
Tell me something, if the molecules of which a wafer is composed are only it’s “accidents” in what is it’s “!essence” supposed to consist?
Essence is an intellectual property; a real property, but one that is not material. So when we know something, it is the essence we are dealing with. There are accidents that are proper to essences, such as flesh and blood for humans (so you can’t have a human essence without these accidents), but the essence doesn’t consist of these elements.
So, to put it simply, the essence of a wafer is “wafer”. The fact that you can communicate “wafer” to me as a real, existing thing without telling me anything about its actual properties illustrates the difference between those properties and the essence. In the case of the idea of “wafer”, flatness could be said to be an “essential accident”, since it’s an accident that is attached to the essential idea by definition, but “flatness” isn’t the essence of a wafer. This is the same as when we know the accident of “red-blooded” when we understand the essence of “human”; it remains an accident, but an accident that follows necessarily from the essence in question.
So one very important thing to understand is that we never deal with essences other than with our intellect; you never physically touch an essence directly, for example. The intellect is the proper “location” of essences, aside from their own individual manifestations, such as this or that rock for the essence of “stone”. So the essence of “stone” would exist either in our mind, or “under the accidents” of this particular rock, but the essence is never measured physically, only analyzed intellectually (so I know what “stone” means, even though the idea of “stone” in my mind doesn’t have any physical properties, but is rather an essence known).
Hope that helps!
Peace and God bless!