I think you're mixing up atheism with the positive worldview that atheists may have, such as philosophical naturalism, secular humanism, scientism, physicalism, liberalism, and so on. Atheism itself is just the negation of theism so it doesn't have much content to be incoherent.
What I think you're getting at, though, is that atheistic models of ultimate reality are bound to be problematic too. And I'd agree with that. I think all knowledge is partly subjective, as long as the knowledge includes our understanding of what we're talking about. We humanize what we try to understand, and humanzing the inhuman cosmos is bound to be problemantic.