What I expected to happen was...:

The tree should grow through the blocks and generate normally, with the leaves becoming waterlogged. It should grow through logs placed above the saplings and replace leaves.

What actually happened was...:
When a pale oak or dark oak sapling is bone mealed so that it grows through logs or leaves and into water, it does not generate logs connecting the point the saplings were to the top of the tree. This happens with all different types of logs, as well as leaves. If the tree grows through water and ends in air, the parts in air generate normally.

This does not seem to affect other 2x2 trees (Jungle , Spruce)

Steps to Reproduce:

1. Load provided structure file, or build a structure so that the saplings are in an air pocket underwater, with blocks they can grow through directly above or 1 block above the saplings, and water is above said blocks
2. apply bone meal to the saplings