I actually thought that tree with the life fruit on it was the precursor to the Great Deku Tree, just purely based on the fact it had some kind of magical property. I think the big tree is just a big tree to be honest but there are similarities.
intresting easter egg that is incredibly ...strange.
In WW, when fighting Phantom Ganon, you can deflect the electric spheres with your bottle.
If, while getting to zeldas room, if you do it at night through the chimmney, when you land on the grate and look down, you will see the Headmaster takiong a bath, explaining why you can't go in there at night.