The central methodological challenge was that cranial morphology — the shape of the skull — is determined by a complex combination of genetic and developmental factors, and that similar skull shapes can arise independently in populations that are not closely related, while closely related populations can sometimes show significant morphological differences due to developmental plasticity and environmental influences.

The observation that Lagoa Santa skulls resemble those of Australian and African populations does not, by itself, tell us that Lagoa Santa people were closely related to Australians or Africans.

It tells us that they shared certain morphological characteristics.

The cause of that sharing — common ancestry, independent parallel development, environmental influences on skull development, or some combination of these — cannot be determined from skull shape alone.

This is not a criticism of the researchers who used morphological analysis; it is a description of the inherent limitations of that type of evidence.