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Perhaps one could punch the two holes separately, so that both jagged edges would be safely on the inside of the folded lid. You'd have to do it before you fold it in half, I guess.
I have fermented garlic before, and thought I'd mention what happened with mine. The garlic cloves turned a beautiful bluish green color. I learned that this sometimes happens with very fresh garlic, and there is nothing wrong with it. In fact, they returned to their normal color after some time.
DON'T use confectioners' sugar! It has corn starch in it and will affect your caramel.
Do you think it would work to wrap the dough over the end of the stick so that one end of the dough tube is closed? If so, then you could stuff it without worry of the filling running out the other end.