I restarted Minecraft PE and the sky was restored to normal.
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.
Yes as of the current build of Minecraft PE 1.21.2 the bottom row of storage chests isn’t selectable. Whether occurring only while using the “Backbone Controller” or on screen controls. Using the “Backbone Controller” to highlight any squares on the bottom row of a storage chest inventory causes it to automatically bounce back up one row above the bottom row of the storage chest inventory.
Also holding down on the controller to highlight (select) the bottom row in the inventory. Will cause it to rapidly stutter but won’t allow you to land on the bottom row. Placing items on that bottom row makes them almost impossible to retrieve without having to break the storage chest spilling out all the items.
I hope that helps.