It is, and of course scientific methods have limits about what they can tell us concerning one-time acts of history, in particular on such a small scale. I might have a some-what broader view than you do about how much they can say, but then it is easy for me to think that- I am not in a field dominated by aggressive philosophical naturalists!
Science may not be able to tell us if this is in fact the genetic signature of Adam and Eve, but it can tell us some things which relate to matters of theology. For example, when deciding whether the scriptures are teaching us that Adam and Eve were the sole progenitors of all mankind, or merely the ubiquitous genealogical ancestor of all mankind, or something else, we can use the evidence that you have shared with us here to rule out the first of those options anytime within the last 50K (or maybe even 100K) years. So if our scriptural hypothesis has an Adam any more recent than that, we must consider one of the latter two options.
In the same way, Y-chromosome data has pretty much ruled out the doctrine that the flood of Noah reduced the entire human race to a single Y-Chromosome anytime in the last 50K years. This pretty much invalidates the Reasons-to-Believe view of scripture on the flood. It does not invalidate the Christ-centered model that I have written about. So while science may not be able to prove a particular act of God or account in scripture as true, it can prove certain ideas about classes of interventions which left lasting traces false.
So the problem is only underdefined if we fail to specify a particular view of Adam which can be measured against what is observed in the lab or in the field. To their credit, RTB produced a testable creation model. To my view even though its confidence levels are not as high as we might like it was robust on its astronomical and astrophysical points but fell down once we get to Adam and the Flood. It was a testable model and the first part passed the test- maybe not with flying colors, but the second part has not passed the test. They need a new model. I have one, and so do you. Others may have yet more models.
So long as they define it enough to test to a similar degree as things that we consider science now (I am looking at you sociologists and theoretical astrophysicists!) then science has a little something to say about theology, even if ultimately God is not going to submit Himself to our lab tricks and is by definition beyond the laws of nature which science is designed to discover. Men cannot expect to discover God strictly through the scientific method, but we discover which of competing views of scripture are more or less compatible with evidence from the natural universe.
The Bible does not directly say that Adam and Eve had a unique genetic signature, but if you hold that they were a special creation after Adam the Race came to be then it is a reasonable inference. If they did, Basal Eurasian looks like a great candidate for that based on my model for time, place, and circumstances. Moreso than I have time to go into here.
Now it could be that this idea will be falsified tomorrow. Indeed when I first wrote the book I wrote that if Kostenki 14 really did have Basal Eurasian genes then the hypothesis that this was the signature of Adam and Even would be falsified. This is because it would have shown that this group was “out there” 30K plus years ago and did not suddenly show up in the crossroads of the world 14K ago! It turned out that it did not - it only looked more similar to basal because it had not gotten to the fully Western-Hunter-Gatherer profile yet. It was “basal” to the East-West split, but was not that basal.
If they find such a specimen for real, it does not falsify the Christ-Centered model, only the idea that this signature is that of Adam and Eve according to the Christ-Centered model. Though I don’t go as far as you do in broad terms I agree with your position that the scientific method has limits in its application to theology and apologetics.