This ''oversimplification'' is definitely not a problem here. It's journalism, it's supposed to be more simplified and even in the article they mention in the first paragraph that it's base modification that they are reffering to with that AND they examplain in tl;dr how it works (so that you know what level science journalism is done on). They could write out that they mean ''letters of the genetic code'' but contextually everyone generally familiar with it should be aware that that's alluded too.

And honestly if you want to be so overprecise on the genetics then saying that they exchanged two amino acids instead of two ''letters/nucleotides'' is practically more ''wrong'' because the difference in aa sequence is a downstream effect of nucleotide conversion and not how mutagenesis principally works.