Indeed, the first chapter of the book of Genesis should make it clear to the reader that he will not be able to understand the words of God by his physical senses and reasoning alone. Ditto for the first chapter of the Gospel of John. And both start with "In the beginning..."
John seemed to "get" the metaphorical tone and intent of Jesus.. Could be not all apostles "got it"(fully).. Surely Saul(Paul) got it..
I know many christians that don't seem to get the metaphorical nature of most of scripture.. I call them "literal" christians.. Don't mean they are not christians just "thicker" ones.. Surely non believers are gobsmacked by scriptural metaphors.. which was the main intent I suppose..