If naturalism is true, it’s a great cosmic tragedy that we’re intellectually equipped to uncover more than we’re emotionally equipped to handle, but it’s not surprising. We’ve evolved to get things done, not necessarily to feel good about our place in the cosmos.
Yep, this is what I've been saying all along.

Humanity would be the great tragedy of naturalism, not necessarily something positive to be celebrated. Life itself takes on an uglier tone if there's nothing to it besides chemical reactions gone wild. And I do agree with your assessment of modern society and psychological issues.
On the other hand, I don't think knowledge of cosmology, psychology, and biology really eat up much room at all. It's difficult to see how life could have ever evolved at all if our universe weren't in some sense seeded for it, if different chemicals didn't have it in their nature to give rise to life under certain circumstances. Science explains how physical reality interacts to produce the effects we see; it doesn't explain why it was the case that it would act this way to begin with. I don't see how it even could. It doesn't say too much about ontology in and of itself--it was a specific Enlightenment era mechanistic materialism that ruled out other options, and that was blown to smithereens with quantum physics. Reductionism is a bit out of style now, so things are opening up again. Or they would be if naturalists didn't have kneejerk negative reactions to the alternatives.
The only genuine problem I see is that the modern understanding of the mind rightly rules out claims of certainty. Can strong arguments for theism be made from logical principles? Yes, but reality ultimately need not conform to human notions of logic. This is a problem for everyone, not just theists, but we've become so obsessed as a culture with certainty, verifiability, and so forth that it looks more damning than it really is. And this is not helped by a certain type of apologist.
I can agree with this, and I think I’ve probably been guilty of overlooking it more than once, perhaps even with you, so I feel I should apologize.
No worries.
That said, if one is submitting an argument in an apologetics forum that’s not explicitly for believers only, they’re fair game to be desconstructed in terms of soundness and accuracy. That’s what an open apologetics forum is for.
Hmm. I both agree and disagree here, depending on the type of argument in question. There are certain arguments that really are aimed at a modern audience: Fine Tuning, certain design arguments from ID, Craig's Kalam, and probably a handful of others I'm not familiar with. Knock yourself out deconstructing those.
On the other hand, there are other arguments out there that are much older and meant for very different audiences. Any of the Greek or Scholastic arguments would fall into this category, and the problem with immediately jumping to deconstruction is that you don't necessarily know what they're saying and why they're saying it. We interpret the arguments in a completely different light than what their original proponents intended, so something like Aquinas's teleological argument gets addressed as if it were a modern design argument, and it isn't. At all. The first step here has to be to try to properly conceptualize the argument and figure out what's going on rather than rushing straight to critiquing it, and that almost always gets skipped. And not just by atheists.