Sure I understand that, and I've already acknowledged in many of my replies that science is useful for answering many questions... but at the end of the day science is clueless as to how we got here and how it all began.
This is why it bothers me when people assume that the atheist position is somehow "more scientific", it's just such a smug take. I have no problem with people taking the agnostic position because that's a completely honest answer, but atheism is just another form of religion, they believe with great ferver that there is no creator or purpose, to the point that they'll ridicule people who do believe and throw out smug comments like "magical man in the sky sitting on a cloud", "believing in miracles" etc... completely blind to the hypocrisy of such comments when your consider the alternative.
At the end of the day if we are being honest, none of us "know" with certainty one way or the other. To me personally the idea of everything from nothing for no reason at all is the least logical scenario, and I choose to live my life as if there is a greater purpose because I believe it brings out the best in me, but if someone can get to the same place without believing in anything then that's fine too.
Atheism like theism is a spectrum, just like in political ideologies, once you move further from the center, the more rigid and narrow your worldview becomes. Atheism (Strong/Explicit) can be considered a belief system if it states that only the natural can exist, if a person just espouses a lack of belief in the supernatural then they are considered Weak/Implicit Atheists.
As far as "more scientific", I'd have to say that Naturalists should be "more scientific" as science and the natural world are all that they believe in. As far as how we got here, there's 2 parts:
1) Life on earth - We have strong evidence for evolution from the earliest known life forms to the present, but we do not have a complete, unbroken chain of evidence all the way back to the first form of life on Earth.
If you're talking about Abiogenesis, then yes it's still in the hypothesis phase and there are several plausible pathways for abiogenesis (e.g., RNA world, metabolism-first, lipid world), but no consensus on which is correct or most likely. The abiogenesis event(s) are proposed to be billions of years ago, and we still are gathering more data, and even though it's extremely difficult it's still possible/probable that we eventually fill in the gaps.
2) How the universe began - with the CMB we can observe the oldest light that dates back a few hundred thousand years after the big bang event. Theoretically we can go back to just after the Planck time by examining the CMB and its dispersion patterns.
If you're talking about the moment of or "before" the big bang then we just don't have any data (and may never get any) and we can only theorize with mathematical models like String Theory and LQG.
So, yes there are things that we may never have any data for and truly understand, but I think that the processes that Naturalism uses are "more scientific" compared to Super-Naturalism (Theism).