When you look at that image, I could see Morpheel bearing a resemblance to an Octorok. I always assumed it was a corrupted Skullfish, because we see several in the body of water before entering the boss room and iirc it releases Skullfish during the battle.
Either way, I agree, I thought TP had a cool approach to bosses. They all make sense and occupy the world, they aren't just random giant monsters with no origin.