Agreed, Is that the video where the guy uses terms like "conspicuous consumption" unironically? If so, I think I watched it too. A lot of retards think that in depth analysis consists of reading way to deep into everything to try and find connections, irregardless of whether those connections actually exist. In actuality, the god killing seen in jrpgs is probably the product of a streak of antitheism which was a reaction to the zealotry that the government tried to foster during imperial japan. During the reconstruction period, the country saw a huge swing left politically, which led to negative attitudes towards things like imperialism, patriotism, religion, etc. But writers were still hesitant to actually start embroiling themselves in ideological conflicts with their mostly non-athiest audience, so criticism of Buddhism or shinto is still pretty rare. Abrahamic religions though, specifically christianity, are widespread enough to be recognized, yet are foreign enough to be fair game. A lot of other authors followed suit, though often more so for the aesthetic than for what it represented philosophically.
An important thing to note though, is that an omnipotent god is obviously unable to be defeated. Therefore if it is defeated, then it was a false god. So you never actually "kill god", you only kill fakes, and what you're really doing in all these games is "proving" that god doesn't exist by destroying a pretender that's called god. Proving atheism essentially, by slaying the dragon of religion. It would be funny if you killed god for real and the universe just winked out of existence because there's nobody willing it to exist anymore, but that wouldn't teach the proper moral lesson now would it?