It could be from Covid, previous TB infection, or smoldering TB. The only way to know is via the well-established TB sputum testing protocol, which is quite routine at Saint Luke's and for Filipino visa applicants.
The source of the scarring isn't really relevant - what doesn't make sense is that it would be given as a reason for inadmissibility. An expected result would be for the applicant to get a 221g pending testing. But as @Chancy points out, someone with a suspected or confirmed TB infection would not even have an interview, as it seems the medical exam is required to be done prior to the interview for USEM (not a requirement for many other embassies).
In the totality of OP's posting history and stories, something here isn't adding up.....