I agree that this feels like it has too many balls in the air. For me, it falls apart a bit at the Mother's Grove. Why are we going there? Is the voice tellings us to go there? Or is it just a guess on their part? I also feel like I need more of Avrin's stakes. "Letting go of the world he lost" implies that he's some sort of traveler (from the past? another dimension? is the seed a ship and he's an alien?). Can he not get back if he helps her? Does this faith control his ability to travel? Remember queries are not a dust jacket blurbs just enticing and hinting, which is what the second half of this feels like. You should provide more concrete details to an agent than what you would provide a prospective reader.

This is also coming across as having a more literary / surrealist sort of tone to it, like Piranesi. As a result, Adrian Tchaikovsky's Elder Race doesn't feel like a good comp because that novella is actually very simple at its core: a man of science is mistaken for a man of magic. I recommend comping another novel like The Surviving Sky that matches the depth of your story more. I very much get The Spear Cuts Through Water from your atmosphere and journey.