A little theory
So I have a small theory on the three gods and three bosses (the three bosses are Three-Eye, Three-Eye's Leg, and Three-Eye's eye) My theory is that each boss you can find in game is like an effigy or simulacrum of their respective god. Intelligent creatures in Noita do seem to build statues, the one I'm most thinking about being the wooden totem on the Lake island. Three-Eye, guarding the Work, is a twisted copy of the god of Magic. It guards the Work and prevents its completion. The statues similar to him in the Laboratory would be smaller, less complex versions. Three-Eye's Leg in the Pyramid is the oldest of the gods and is found in the Pyramid, described as the "pinnacle of past civilizations" by one of the books. I find it unlikely it would be the actual god due to its grotesque shape of green slime and bones, and the fact it is resting on an altar with glyphs that read "YOUR REWARD", so it was likely made by an ancient civilization, maybe pre-alchemist, that saw Nature as the greatest. The wizards of the Magical Temple likely saw Magic the greatest. The Three-Eye's Eye in the Power Plant is the effigy of Technology. It initially is in a large circular area, similar to the Robotic Egg, but lacking in complexity. Technology likely created the Power Plant along with the gift of machinery. Technology's effigy in this case would be an attempted reproduction, either created by Technology himself as perhaps a reminder or puppet, or created by a civilization such as the Hiisi, who probably see Technology as the greatest.
TL:DR Three bosses are reproductions/totems of three gods, each created by the faction that would revere the respective god they are above the others. Alchemists/Wizards: Magic, Pyramid civilization: Nature, Hiisi/Robots: Technology.
P.S. The Pyramid does contain Wizards and other enemies that would worship Magic, but I believe the Pyramid's ruins (magic exists, even if the ancient civilization praised Nature they could still use Magic) would have been repurposed, or even a model for creating the Temple of the Art and similar. Additionally, the Orb on top of the Pyramid has remarkably smooth brickwork compared to lower down the Pyramid's slope, suggesting a force that could hold up such an old structure without collapse. Also, the traps in the Pyramid would be put there by Hiisi, because Hiisi Alchemists can spawn in the Pyramid, or by Technology.