No 3rd party app was used or any other app modification. These air pocket and grass structures under water were discovered in the official Minecraft PE iOS edition on survival mode.
On looking closer, based on the grassy patches and elemental properties. The boxy structures are most likely air pockets in a section of the map that was supposed to generate above water.
That would also explain why my character couldn’t swim back through them to reach the surface.
I restarted Minecraft PE and the sky was restored to normal.