I'm often not this meta with the strip, but even Adam himself can't get around the fact that this story feels metaphorical. How could you take it literally even if you were involved in it yourself in real life? It would be like if your parents told you, as a kid, to stay away from the Cookie Jar of Free Will and Consequences.
Another way of showing that the tree was beyond a regular tree was to make sure I pointed out what the Bible actually says: that God himself planted the tree. This either means that God was human-like and able to plant organic trees, or it meant that the tree was a magic, godly tree--made of spiritual stuff. In other words, metaphorical. It comes from the "deep magic from the dawn of time."
Thanks to John Milton, people tend to think of the tree as containing apples. When Milton wrote Paradise Lost, the word apple was a generic word for fruit, and since people get their Genesis from Milton more than from the Bible itself (whether they read either one of them or not), apple (as a specific fruit) stuck. I drew all kinds of fruit on my tree, to show that it didn't matter and to show the multi-faceted nature of the tree. I also wanted it to look otherworldly and pretty: tempting.