First of all, you shouldn't be able to see the roofs of the buildings in Ilex Forest to begin with.
In HG/SS, its not possible to fly in Ilex Forest, yet for some reason, you can fly in Ilex Forest in Pokemon 3D. I guess this minor detail was overlooked.
A sign in Ilex Forest specifically states "Ilex Forest is so overgrown with trees that you can't see the sky". I believe from that explanation, its quite clear that flying in Ilex Forest would likely cause you to crash into a tangled mess of tree branches, which is why you can't fly in that map.