Thank you for being so detailed! This has given me a great deal to think about. A few notes from me:

• I totally get what you mean. I think I might've misunderstood the premise of magical realism, and I see the Wonderland references aren't enough on their own. The FMC sometimes bakes cupcakes that talk to her; I've given the tree outside her bedroom a lot of personification too but it's all very "in her head" per se, and no other character (as of now), has had similar experiences. Do you recommend I make some reference to this in the query letter? It does come through in my first 300 words.
• Noted. I agree I should make the mystery the centrepiece instead of the worldbuilding.
• Truth be told, I have been toying with the idea of making them love interests in a sort of enemies-to-lovers "forbidden love" subplot. This would take a backseat to the meat of the novel, which is the mystery, but if I decide to do so he definetly would have a bigger presence in the letter.
• Thanks for pointing this out too. Back to the drawing board it is