Voyage of the Dawn Treader is my favorite too. I never got familiar with any theories, I just see the Dawn Treader itself as loosely representative of the Church.
Aslan’s tearing off of Eustace’s scales always moves me deeply. As does his simple message to Lucy in the hour of her greatest despair: Courage, dear heart. And I think Reepicheep’s quote is my favorite out of all fiction:
My own plans are made. While I can, I sail east in the Dawn Treader. When she fails me, I paddle east in my coracle. When she sinks, I shall swim east with my four paws. And when I can swim no longer, if I have not reached Aslan’s country, or shot over the edge of the world into some vast cataract, I shall sink with my nose to the sunrise.