The fact that different methods point to the same result, even before DNA-sequencing, is pretty strong evidence that the conclusion of common descent is warranted.
Common descent is best scientific explanation, but the truth could be quite different and beyond scientific explanation. We'll never know the truth.
Consider an object in a sealed box. Evidence can be gathered as to what the object might be, but without opening the box, the truth of what the object actually is can never be known.