I don't understand how you arrived at that meaning for "made of". I have an automobile that is made of: steel, glass, plastic, iron, leather, cotton, rubber, copper, tin, and much more.
"Made of" and "made from" seem to have the same meaning.
"Wine is made from grapes" conveys the meaning that grapes are no longer recognizable in their original form in wines.Wine is made from grapes, meaning that grape is the only element..