A man like me has trouble understanding this question. As a native speaker, I cannot understand the confusion.
As the example above shows, the prepositions "like" and "as" are not limited to forming similes. They have literal use.
There is nothing that prevents the literal, ordinary use of such preposition within an extended metaphor:
He's a bird in the morning, but a worm come the evening. As a bird, he flies high in the sky. He could be anywhere. Before the sun sets, he buries himself in solitary darkness, going nowhere, seeing nothing.
Without context, your third example doesn't manage to establish a metaphor. In the context of a fantasy (say, one in which wizards can change shape or ghosts can possess animals) the statement can be easily taken as purely literal. In a more prosaic context, it can be read as the sort of explicit comparison known as a simile.
We use "metaphor" to mean an implicit figurative comparison. We use "simile" to mean an explicit figurative comparison. This means that you cannot use the word "as" to establish a metaphor. When it establishes a comparison, that comparison is explicit. When it does not establish the comparison, that comparison may be implicit and therefore may be a metaphor.
That the words "like" and "as" establish similes is a good rule of thumb, but it's not a law of nature. "He eats in the manner of a bird" or "She sleeps the way a cat does" manage to stand as similes without using those magic words. The notion that similes use "like" and "as" is much like the notion that nouns are people, places and things -- a reasonable approximation when you're first learning to identify them, but an approximation that you're expected to leave behind once you gain a deeper understanding.