Nope - the restriction sites aren't in the final assembly in that paper. These authors just don't understand the tools remotely well enough to have written their paper. It will never be published.
Yeah, I think Kinney is wrong here. Someone else found a survey paper noting the theoretical possibility of using BsaI and BsmBI in a way that leaves the sites in the final genome, but I haven't seen anyone who actually did that. So I'm leaning to a false discovery here.