What makes a bottle to be a bottle? The matter that forms it can't represent the actual bottle without the substantial form of a bottle. On the other hand, the substance itself of the bottle has an accidental form. So what exactly happens when the bottle falls down and breaks into small pieces? Is it an accidental change of the form of the substance (Aquino's 'dough' example) or is it a substantial change that leaves behind only the matter of the bottle?

Here's one quick answer to your first question: What makes a bottle a bottle (more precisely: what makes something a bottle) is whether someone uses it as a bottle, not what it's made of or what its form is. Although the rest of your question is stated in Aristotelian and mediaeval terms of substance and accident, I think that part of your question concerns the nature of artifacts. On that topic, you might take a look at my colleague Randall R. Dipert's Artifacts, Art Works, and Agency (Temple University Press, 1993).

Read another response by William Rapaport
Read another response about Existence