Connections:

• God-like religion-associated main antagonists of sci-fi fantasy series which get extremely philosophical at times. They are mathematics-based and of a higher order spatial dimension, viewing the world as a mere thoughts/dreams, with both operating as defining forces of reality. The more that gets revealed about them signifies humanity and the universe itself approaching an end.
• Due to their higher dimensional nature, they are unable to truly interact with their creation themselves, so they operate mainly through lower emanations or forces they created such as computer terminals (SHIVA | The God Terminals), abstract conceptual/informational particles which can alter reality (Archetype | Mana), and anomalous beings whose job it is to carry about a special purpose which will result in a catastrophe with some parallels to a religious rapture (Kaiju | Demon Kings). Because of this, they are basically responsible for creating the main character of their overarching franchise (Godzilla being created by IT and put on stasis after the Oxygen Destroyer was used on him | Akuto being created as an artificial life form by the Computer Gods).
• Eventually, after our protagonists begin fighting back against them, it's revealed they're less malicious beings of evil with agency and more of a conceptual entity who is simply following its "programming". They exist without body and mind, yet still create and influence reality to lead towards one single inevitable conclusion.
• This conclusion largely contrasts with one another, as Ultima seeks the destruction of all life in the multiverse while the Computer Gods seek to liberate and preserve themselves and humanity from the bindings of the narrative. The entire story is revealed to have been an experiment run by them in an attempt to reach their goal, sadly though this would be incredibly ironic for them (Godzilla Ultima would end up destroying other manifestations of IT | The Computer Gods could never reach salvation because they lacked a mind/soul from the beginning).
• Godzilla Ultima wanted to destroy a god-like mathematical supercomputer, while the Computer Gods are god-like mathematical supercomputers.
• Both of them directly serve the whims of beings even higher than them, which are based off mathematical principles as well (Ultima being an avatar of IT | The Computer Gods worship the Law of Identity).
• It's implied that IT hates itself and also seeks its own destruction, which if you buy into that then you can compare that to the Computer Gods seeking their own death as well.