If I understand Dr. Swamidass's suggestion, the scientific evidence is consistent with the possibility of a large pre-Adamite human population, but also a recent creation of Adam and Eve to which we could all trace our ancestry.
What would the theological problems be with such a scenario? One of them might be the spiritual status of the pre-Adamite population. We need not assume that this population was in some way less human than Adam and Eve. It could be that they were every bit as human, physically, mentally, and spiritually. If so, what would have been the point of a recent, special creation of Adam and Eve? One idea that comes to mind is that It could be that this was God's initial step in the redemption of humanity. Perhaps the pre-Adamite population had already been tainted by Satanic influence. If so, then the creation of Adam and Eve was the beginning of God's redemptive act. If Adam and Eve had resisted Satan's temptation, would they have been able to redeem the rest of the human race in some way? We don't know. Adam and Eve did not resist temptation. Yet, even so, we are told in Genesis 4:26,
"At that time people began to call on [or proclaim] the name of the Lord [Yahweh]."
So there would at least be the positive result of introducing knowledge of the true God. And from Adam and Eve would come Abraham and Sarah, with the miraculous birth of Isaac, and eventually the miraculous incarnation of Jesus, the Son of God, through whom all peoples (even pre-Adamites) are blessed.
So if Swamidass's suggestion is correct, we can see how it would fit into a certain pattern consistent with Biblical revelation.