The Super Robot, as a concept in fiction, uses the same narrative structure as a superhero. This also means that its roots are the same: mythology. The biggest icon of Super Robots--Mazinger Z--explicitly acknoledges this fact at multiple levels. The name means "Devil God", the catchphrase is "I can be a god or a devil" (refering to the robot's power being subordinate to the pilot's morality), the origin story involves Ancient Greece, several villains are re-imagined gods or monsters (not just Greek), and the 2009 retelling (Shin Mazinger Z: The Impact!) even has Zeus appear as both an ally and a material source of the title robot's power (coupled with the fictional Unobtanium power source, Photo Power).
You see similar use of mythological motifs, themes, etc. with all of the successful and enduring Super Robot properties. It's not just because they were early; Tetsujin 28 was even earlier, but nowhere near the juggernaught status that Mazinger Z attained. No, it's because they embraced the mythological roots and used them to tell as powerful a story as they could. In time, Super Robots attained an iconic status that few Real Robots match- and one of those Reals, the RX-78 Gundam, is a retooled Super design.
The Super Robot is not a prototype for a mass production design. The Super Robot is not a customized machine for an ace pilot. The Super Robot is a heroic icon in its own right, and the pilots that sit in its cockpit are the partners it has in executing its core mission. In this respect, the Super Robot is a technological manifestation of the Iconic Hero and his Core Ethos: Mazinger Z is the premiere warrior defending Mankind from the evil traitor Dr. Hell and his horde of Mechanical Beasts (or later the reborn Mycenian Empire under the Great General of Darkness). Getter Robo is the Champion of Life against all that oppose it and its chosen species: Man. Grendizer is a Superman figure defending Earth from the aliens that destroyed his homeworld. You get the picture.
If you think this would not be willfully wielded for deliberate effect, you would be sadly mistaken. If you then think this cannot be so used for good ends, you're doubly-mistaken.
In the far future of Galactic Christendom, this knowledge was not lost.
The Church, knowing how Mankind thinks, used breakthroughs made in the City of God to make real the fictional Super Robot of pre-Cataclysm popular culture. This was not a thing done out of whole cloth. It was a new form of the same use of iconography and psychology that lead to the early post-Cataclysm efforts to contact survivor communities and begin to knit them back into a greater whole, originally called "Project Gandalf (after the Wizards of Middle-Earth and their mission).
As the Dark Lords revealed their true forms and more of the Nephilim stepped out of the shadows, the pre-Flood abominations also stepped out and the survivors--and later, their children and grand-children--saw things in terms dervived from pre-Cataclysm entertainment: Kaiju, Titans, Mutants, Dragons. It took time for the legendarium of old to reassert itself, and as destruction is swifter than healing the Church had to use the language at hand to deal with the issue.
Giants require giant-slayers. Monsters require monster-slayers. Terrifying monsters require heroic warriors to slay them, and--and this is critical--be seen doing it. Men need to be reminded generation after generation that monsters can be slain by ordinary men because there is a constant flow of new generations that come forth and need to witness this truth to comprehend it. Heroic icons, therefore, have a lawful purpose on multiple levels.
This is why the Super Robots exist, and why they are so powerful: they are the heroic icons that go forth to face the monsters that threaten Mankind.
The breed of men that mount up, get in the cockpit, and go forth must be the very best available and not just in strength of limb, but of heart and soul also. Those men made the difference with the early models of Super Robot, and as the reconquest of Earth turned into the Liberation Crusades that pushed the enemy off-world and then out of the solar system the model for not only the Star Knights but of the various noble houses was made and struck.
The Super Robots would go on to become the icons of noble houses, giving them an anchor for the identity of entire nations. They would define the Church's elite heroes. They would be more than just great war machines, but achieve the full morale-boosting power and narrative weight that their iconic status enabled- and so would those chosen to pilot them.