I emailed Miller a while ago to see what he thought of this reply, and he thought it also seemed like a reasonable approach. But, in his view, the criticisms of his method within their framework include things that in practice he sees as features. In particular, they view the bias caused by using the lower bound as a bug, but he prefers rankings to be be "risk-averse" in recommending, avoiding false positives more than false negatives. Of course, that biased preference could also be encoded explicitly in a more complex Bayesian setup, which would also be a bit more principled, since you could directly choose the degree of bias, instead of indirectly choosing it via your choice of confidence level on the Wilson score interval.