I think the "making sense" refers to the fact that "billion" has "bi-" as a prefix, and "trillion" has "tri-" as a prefix. In American English, it's not clear what is "bi-", exactly, about a billion -- two of what?

If we had skipped "billion" and gone with "trillion" = 1e9, then it would be more natural, because then it would refer to the number of thousands; but then the more natural nomenclature would be "bi-sands" and "tri-sands" or something.