The Irony in Atheism

As I continue to read Bakunin's writings, I find a man who prides himself in logic and in his extensive knowledge on the existence of all things. In this way, I feel like I somewhat relate.
However he seems to be an Atheist, like many of my friends are, and every time I come across someone who believes that way, the same question nags me to the point of insomnia (like right now).
But before I expose the question, let me expose my foundational premises of why science and evolution has such difficulty answering it.

1. Science is systematic knowledge of the physical or material world gained through observation and experimentation. (From Dictionary.com -my fastest online resource)
Thus science cannot use metaphysical components to answer its questions.
If a scientific question is asked it must be answered with scientific components. If the answer turns out to be a metaphysical one, than the question was always metaphysical.

2.In science everything has to have a beginning, because it is systematic.

3. Anything eternal is metaphysical.

Here is what I mean: If the scientific question is "How did the universe (every physical matter that we incorporate in science) begin?", then science has to prove it using non-metaphysical components. If science says that it was created by God, it would break the main premise because God is metaphysical. So I concede that through science, nothing metaphysical can be proved or disproved, according to today's definition of science.

However the question "How did the universe begin?" seems to be answered, even in science, with a metaphysical answer. Because anything eternal is metaphysical, if time and/or space were deemed eternal than it is out of science's realm.
So the only way for science to be given the opportunity to answer the above question, is to show how time/space could of come about by itself.
But, even before that, can one even imagine a point in time where time didn't exist? Even imagining that, seems to be an impossible task.

Try imagining a point in time space didn't exist? When I imagine the Big Bang theory, I always imagined that before the universe was birthed, space was present... it was just empty black space, like inside an empty jar in the dark.
It seems as if we all concede that time/space is eternal. Even if the earth were to disappear like it appeared, space and time to do the same doesn't seem reasonable or imaginable.
If in fact time and space are believed to be eternal, than the red flag goes up stating that, the answer to our existence has to be of metaphysical kind. Because what seemed to be a core truth of our physical world, is actually found to be of metaphysical origin.

If a man were to just appear, not ever having a mother or a father, not ever being a baby.... but just one day appear, science would not come close to explaining it. But, some religious people might have a field day saying things like "It is a miracle" or "Our new prophet has come". And rightfully so, because the question "how did the man come into existence?" would have to be answered with a metaphysical answer, because it denies our scientific laws.
If scientist would never attempt to explain how a man out of no where, from nothing, just appeared as a human, why then does science try to explain how time/space/inorganic/and organic matter come into existence?

It seems as if Atheism allows for the metaphysical world that it so adamantly rejects.