You are correct. John does not have the account of the Last Supper in his Gospel. But remember that John was writing much later and was writing theology. He had the synoptic Gospels and some of the writings of St. Paul in front of him.
John, supposedly, lived to a ripe old age.
So, Chapter 6 of John is the Discourse on the Bread of Life — explaining the Last Supper to those who were not present. Some listened and their hearts were changed. Some had hard hearts and walked away. Note that Jesus didn’t call them back and say something like I was only speaking symbolically — he lets them leave.
From your perspective, you don't find it extraordinary that John felt the need to "instruct" about the Last Supper in John 6 but then does not even mention it during the events which surround the passion? The Upper Room Discourse? I think you have to look for another explanation for John 6, the symbolism does not fit the context or the later developements of the book.