You may presuppose anything that you wish, until you test it against harsh reality and run the perilous risk of showing it wrong.
Presuppositional apologists ignore the above statement, as though any assumption were as good as any other, when in fact most of what we often assume true, when objectively examined and tested proves to be mistaken.
They do, of course also argue for the superiority of their position using scripture as their evidence, presupposing its infallibility in a delightfully quaint act of question-begging.
Apologists claim that mainstream science, or “Darwinian evolutionism,” “Darwinism,” and other variants, an imaginary religious ideology opposed to their own, presupposes, as they presuppose the Truth™ of scripture, the non-existence of the supernatural and thus their God as an ontological position.
In so doing, they confuse methodological naturalism with philosophical naturalism, the position that physical reality is all that there is.
Methodological naturalism is a working principle, an assumption of procedure that requires the use of natural explanations for natural phenomena, not limited to macroscopic material objects, because such explanations and their implications can in principle be tested.
Science also uses two other principles,  that an objective, external reality exists, and depending on this,  that this reality is knowable and understandable.
There can be no useful science that rejects these principles, since it depends on public confirmation of its facts and a reality in which these facts can exist, and to paraphrase Arthur C Clarke, facts that cannot be independently confirmed do not exist.
This is true even of facts pertaining to subjective brain states, which can be monitored with increasing precision using current technology such as PET and fMRI scans, though these may not be situationally available.
However, even lacking such equipment, some brain states, such as those associated with mood disorders, hallucinations, delusional conditions, and many forms of neurological damage, disorders and pathologies, produce identifiable behaviors or apparent symptoms that can be clinically diagnosed to varying degrees of accuracy.
So even facts of the mind can be objectively if indirectly observed and validated.
Science refrains from seeking supernatural explanations involving omnipotent beings, be they magical gods or universe-creating Intelligent Designers of the technological ET variety.
I’m reminded of Shermer’s Last Law:
“Any sufficiently advanced extraterrestrial intelligence is indistinguishable from God.”
Supernatural hypotheses involving omnipotent beings, even those posed as though they were naturalistic, produce no meaningful predictions, no real difference between observable results whether they are correct or spurious, and science needs to tell between degrees of probable correctness and wrongness, the grain from the chaff, the real from the unreal.
“What would life look like if it were created by an intelligent Designer?”
The answer is that it would look like whatever it looks like.
With a supernatural explanation, we cannot ask questions on the nature of the designer, we cannot ask by what process life was designed, what laws were employed, what criteria governed the design process, and so on.
As an explanation, the supernatural tells us nothing of any use.
While supernatural hypotheses aren’t useful, or even interesting, supernatural claims are fair game, and many have been looked into by skeptical paranormal investigators and mainstream researchers over the decades.
Using supernatural explanations would halt all inquiry, since once you hit upon quick n’ easy magic as the answer, psychologically, there’s no further inclination to look.
Methodological naturalism is a rule of procedure, not an ideology saying that there is no God.
Science has copious evidence for the usefulness and effectiveness of it’s assumptions, even failing the ability to objectively prove its own rules by logical necessity — It doesn’t have to since that’s not what science is for, and it makes no claims of metaphysical certitude for its rules or its findings.
Science has rules it must obey, assumptions it needs to function, a philosophical underpinning it needs to define how it works and what it can find out, but the rules and assumptions of science do not have to obey themselves.