Well then this demonstrates that the dna was simply a atomic manifestation of the biological change from placental to marsupial.
DNA phylogenies are based on a combination of highly conserved areas where homologous function is identical between species, and non-coding regions that vary on the basis of random changes, not as a result of variation in body plan or shape.
So, no. The DNA being looked at in this case can't be a "manifestation of the change from placental to marsupial", because the DNA being looked at doesn't contribute to the placental or marsupial characteristics of the compared species.
Biologists aren't stupid. They knew to look at and compare DNA sequences that were insulated from selection and morphological change.