As I’m setting up these analyses, I have already identified the main problem - the codon tables they used for the snakes (Naja atra and Bungarus multicinctus) are highly biased. Specifically, these codon tables are built on only 57 and 59 CDSs, which typically leads to completely wrong estimates of codon adaptation (which is how they link nCoV to snakes). Compare this to the human codon table (93487 CDSs) or Chicken (6017 CDSs - a notoriously badly undersampled genome).
Given how many genes snake genomes have, one can’t possibly create a representative codon table from less than 60 genes.