Rather than fisk Jeremey's post point-by-point (an exercise which is perhaps even more tedious to read than to write), let me explain some basic metaphysical issues about atheism.
Jeremy gets one thing right: Strong atheism is defined to be the belief that no God exists. "Exists" is the key word here; I'll return to this statement in a moment.
Jeremy's is mistaken that atheism entails a rejection of metaphysics in general:
[A] casual examination of atheism reveals a pseudo-religious affirmative belief in metaphysical constructs, the lack of empirical evidence for which undermines the scientific posturing that buys atheism its very credibility.I've seen this argument before, and it's misguided. It's most probably caused by the assumption that atheism somehow depends on Logical Positivism.
As I discuss in more detail in my essays on The Scientific Method, The Logical Positivism of the Vienna Circle is a failed philosophy. It is internally contradictory and viciously circular. To get to a workable philosophy, we need to go to Popper and the demarcation criterion.
Popper's demarcation criterion differentiates between categories of meaning: statements that are in principle falsifiable by observation have scientific meaning; statements that are not falsifiable in principle have (or can have) metaphysical meaning. It is important to note that the demarcation criterion has, according to its own definition, only metaphysical meaning.
In the passage quoted above, Jeremy conflates atheism, Logical Positivism and Metaphysical Naturalism. Atheism (strong atheism) is only the belief that God does not exist. It doesn't matter why one believes that God does not exist: If you think Richard Dawkins is a prophet and every word he speaks is true by virtue of him speaking, and you believe that no God exists only because Dawkins says so, you're an atheist. A foolish atheist, to be sure, but still an atheist.
Atheism is not even (or necessarily) a metaphysical principle. I suspect Jeremy is trying to talk about Metaphysical Naturalism, which is a metaphysical system. It's a metaphysical system that many atheists actually hold, and the truth of "no God exists" is—for particular definitions of "God"—a conclusion from Metaphysical Naturalism applied to the evidence of our senses. For other definitions of "God", "'God exists' is meaningless", is a logical conclusion of Metaphysical naturalism.
Before I move on, let me recap: Atheism is just a particular belief, regardless of its metaphysical provenance. Logical Positivism is an internally contradictory metaphysical system that no one (or very few) actually holds. Metaphysical Naturalism is one metaphysical system from which atheism can be concluded. Metaphysical Naturalism is a metaphysical system, it is not the rejection of metaphysics.
We can extend Popper's demarcation criterion to the (metaphysical) definition of ontology, i.e. statements about existence: A set of statements about existence is meaningful if and only if the set as a whole is falsifiable by observation. In other words, according to Metaphysical Naturalism, all ontological theories are scientific. This specifically ontological formulation avoids the self-referential paradoxes of Logical Positivism; we must bite the bullet and accept at lease some metaphysics.
Hence the atheists complaint that "Christianity can’t be disproved! It’s made to be non-falsifiable for just that reason!" Jeremy is conflating metaphysics with ontology: "God exists" is an ontological statement precisely because it includes the word "exists"; if the statement (or the theory, the set of statements which includes "God exists") is not falsifiable, it is not, according to Metaphysical Naturalism, ontologically meaningful.
This observation does not merely demonstrate that Metaphysical Naturalism is different from theistic metaphysics. They are different, but all sane theistic metaphysics include Metaphysical Naturalism as at least a special case. The principles of Metaphysical Naturalism underlie all of our beliefs about ordinary reality, not to mention our scientific understanding of the world. If you believe all the ordinary things about the prosaic reality of rocks and trees, if you keep your eyes open and on the road when you drive, your beliefs about reality can be expressed according Metaphysical Naturalism, and cannot be expressed if you contradict Metaphysical Naturalism. A sane theist—and almost all theists are demonstrably sane—can extend Metaphysical Naturalism, but she cannot contradict it.
It is to the extension of Metaphysical Naturalism that those who do not extend it employ Occam's Razor. In order to have "God exists" as a meaningful statement, the theist has to have two accounts of ontology: an account identical to Metaphysical Naturalism to discuss statements of existence pertaining to ordinary reality, and a second account—incompatible with the first—to discuss statements of existence pertaining to God.
There are two problems with this tactic: First, why have two accounts of existence in the first place? Second, the connection between this second account and epistemology, i.e. statements about knowledge, becomes very unclear: How do we know about the existence of this God or any true statements about him/her/it? Since Jeremy is talking specifically about unfalsifiable conceptions of God, we cannot rely on the evidence of our senses.
There are two tactics to give some epistemic basis to statements about God: Either hoist all the statements about God to metaphysics, or metaphysically hoist a particular text as an epistemic basis and making it scripture. Other than severe problems with using a text as scripture (on which, with all good luck, I'll write on soon), Why do this? There's just no need to add anything to Metaphysical Naturalism.
Of course, if a theist wants to extend Metaphysical Naturalism, she's free to do so. It's a free country, and you can believe anything you want, no matter how ridiculous or nonsensical I personally find it. But one is also free to not extend Metaphysical Naturalism, and unless someone can show me an actual need to do so, I reject the charge that not extending it is in any way bankrupt, dishonest, or incomplete.