At the very least, all naturalism—methodological and otherwise—implies atheism. And most fervent believers in naturalism agree with this.
But even if “methodological naturalism” is not necessarily atheistic, there is a problem: if the Bible is true, then the natural system—which appears in its usual state to be a closed system—experienced an act of interference from outside the system when God the creator sent his only begotten Son to die on the cross and to be risen on the third day. Among many other supernatural acts.
In other words, if the Bible is true then the so called boundary between the natural and the supernatural is temporary at best and imaginary at worst.
I'll say it again: that is a lie, it is a Big Lie, and if you keep repeating it, will make you a Big Liar -- so you must stop with that.
Again, the truth here is simple to see, if you just remember that our word "science" comes to us from our Founding Fathers' Age of Enlightenment term "natural-sciences", which for them in no-way, shape or form implied atheism.
They were all at least deists, and most devout Christians, who looked on their "natural science" as a method for learning how God created and runs the Universe.
Their understanding today goes by the term "methodological naturalism" and it is not, never was, never will be: atheism.
After our Founders' Age of Enlightenment came other ages -- darker, more wicked ages -- which go by names like "Romantic", "Modern" and "post Modern", each retreating further and further from acknowledging God's role in science and their own lives.
And so, what began as our Founders' "methodological naturalism" eventually morphed into atheism under names like: "philosophical naturalism", "metaphysical naturalism" and "ontological naturalism".
What's most important to comprehend is that these new terms are not scientific terms, instead they are effectively religious terms describing the religion of atheism.
So please, I beg you: do not conflate & confuse the methodology of our Founders' "natural-sciences" with the atheism in today's "metaphysical naturalism".
I promise: you don't have to lie to tell the truth about your religion.
reasonisfaith: "In other words, if the Bible is true then the so called boundary between the natural and the supernatural is temporary at best and imaginary at worst."
Imaginary, temporary or otherwise, doesn't matter for purposes of scientific inquiry.
Natural-science is simply our agreement to ignore for scientific purposes all except natural causes for natural processes.
This allows scientist of all (or no) religious beliefs to work together on projects and prevents their results from intruding on theological issues.
That atheists have used this agreement to assert: "only the natural-realm exists", is unfortunate, but we don't have to agree with that to support natural-science.