When a block is considered "waterlogged", the hitbox used is that of a full block even if the block is partially transparent. The best example of this is a fence. When placed in water and after attempting to place another block behind the fence (from a position that would not interact with the hitbox of the fence), the block is placed on top of the fence as though the hitbox was occluding that of the one behind the fence. This behaviour was possible before the implementation of waterlogged blocks and should still hold true. Water should not technically have a hitbox.

The attached images better describe this issue.