Undoubtedly after looking at the sequences of that paper, there were some alignments, but how they were structured doesn't point to being engineered, but rather of co-infection, which did not match the conclusions of the paper.
What they do actually indicate might even be more politically inflammatory. That the virus evolved out of a recombination event in an HIV infected person infected with a SARS-like virus, and repackaged as a new SARS-CoV-2 virus.