I wondered about this myself, but in the second sentence of the Abstract the authors say: "This notion [that TB was introduced post-contact], however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World." As you speculate, wouldn't the aboriginal inhabitants be more susceptible to TB from Europe even if it was the same disease, but separated by perhaps thousands of years genetically.
PBS claims that by the 1900 one-seventh of every person that had ever lived had died from TB[1], and according to The World Health Organization, "About one-quarter of the world's population has a TB infection, which means people have been infected by TB bacteria but are not (yet) ill ..."[2]
Significantly, The WHO goes on to say that lifetime risk of falling ill with TB if infected is between 5 and 10 percent. The poor treatment of the aboriginal peoples alone could have caused an epidemic of TB illness due to the crowding, malnutrition, and forced displacements.
My own father had TB, I wasn't allowed to visit him in the hospital as a child that year. Fortunately, he was able to obtain the relatively new antibiotic course of therapy in the early 60's that enabled him to be cured over a long period of time.
See also the Canadian Public Health web page on TB and Aboriginal people [3].
[1] https://www.pbs.org/wgbh/americanexperience/features/plague-...
[2] https://www.who.int/en/news-room/fact-sheets/detail/tubercul...
[3] https://www.cpha.ca/tb-and-aboriginal-people