I'm very sure Gaius came to the conclusion that there is a lot more to the gods (at least some of them) then the Garleans think there is. Probably even more then most people who are religious think there are.
It's only a few scenes after Gaius wonders about what makes the Warrior of Light strong, then he finds out that even Lahabrea, as powerful as he is, worships a god of his own. And that Lahabrea wants to bring about the return of that god for the express purpose of killing the goddess we worship/work for. The Lahabrea broke the world somehow and claimed to have weakened our goddess. And then Gaius watches us fight and beat both the thing Lahabrea used the break the world and Lahabrea himself. So even if we are relying on a goddess for strength somehow, it's clearly working out for us.
In fact, the last thing Giaus specifically tells us is not the our strength is based on something false. Instead it's about how it's people under a weak ruler who have to rely on a "higher power" for strength and how and why that doesn't work. And then he says we are someone who is strong enough to rule. The implication (probably) being, the people who are under us (the Eorzean Alliance) have a strong leader and so they aren't looking to a higher power for strength.
Given what we now know about the Garlean Empire, I could see the commentary about people under a weak ruler relying on a "higher power" applying to it. The Garlean people, even Varis, seem to believe in the "higher power" of Garlean Ideals. True, it's not a god in the traditional sense, but it does seem to be something bigger then them. And we've seen how finding out who those ideals came from has affected Varis. He wants to make those ideals "true" which implies they were not true or a fake this entire time. Which is exactly what the Garleans think about other religions and gods... going by Gaius' reasoning, the Garlean Empire could be considered to be under a "weak ruler" and Solus all but admits he was doing that on purpose.



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