My first quibble is that if you're used to a triple-omni God, the fellow in the story is a pathetic excuse. He dodges the question of whether he's God in his home universe. He has a lot of power, but he understands our universe on such a broad statistical level that he can't or won't use it in detail. The same goes for omnibenevolence, only more so.
I wouldn't mind growing up to be the likes of him, and thinking that one is more important than one is seems to be pretty common among humans and might be conserved, or claiming such might be an intelligence test that the human failed.
I'm an agnostic-- if it had been a "Yay, agnosticism" story rather than a "Yay, atheism" story, it would have been more like "I'm probably the nearest thing to a God you're got".
I don't have a strong opinion about evolving to be invisible-to-humans energy beings. I don't think living organisms of that sort are supported by current physics, but it's plausible that strange things will be found to be true, and it's definitely good enough for a story.
Not a quibble-- the idea that methods of destroying the human race will be found which can be used by individuals fits neatly with my spam variant of the Fermi Hypothesis. It's natural for Fermi to have been concerned with atomic war as a filter.
I think Ben Franklin would have been delighted at the idea of what adds up to a high proportion of individuals having home printing presses and effectively free post offices. I don't know whether he would have thought of the more negative implications.
Spam has been put pretty much under control, though the social cost of spam is high. If it weren't for spam, we'd have email directories, and I don't think the cost of communication which has been indirectly blocked by protection against spam is especially low.
I'm not looking forward to the effects of home virus kits, and I believe they're just a matter of making current scientific tech cheaper.
What do you think about the details of the story?
Do you think the God would claim omni-benevolence? I didn't get that impression. In fact, I'm not sure that the entity would even claim benevolence. As you implicitly noted, that begs the question why to name it God.
Talking with God is a pleasant and inspiring transhumanist short story. I've got some quibbles, but I'll save them for the comments because I think the story is better without spoilers.
There's a discussion forum at the story's site.