I don't have screenshots currently, but the effect is most obvious if Link swings his sword directly at the treeline. I believe if you use the tiles for that as you have them, it'll look like the sword goes over the base of the tree and then dips under the middle part oddly (as opposed to how Minish Cap has it, where the leaves of the tree are all in a top layer and the sword goes under it normally. Outside of the sword this might also show for projectile items and possibly Link himself depending on where he is (if going into the tree, or if at the "hop" of his walk animation the tip of his hat might peek under the treeline).
I'll try and get something to you this week about that (busy with work) - but again it's minor. I didn't mean to seemingly detract so much from the quality of your tile-mapping tool achievement which is pretty neat and awesome.