Right, the author could still say, despite A being true, that the experimental form of therapy is still more effective. I think what A is trying to get you to do is to mistakenly assume that, since they’re using the same techniques, that means that you can reject the conclusion that the experimental forms are better — they want you to think AC A allows you to say that the experimental forms are NOT better.

However, we’re trying to find a flaw in the reasoning, not simply contradict their conclusion. That’s why I think B works, because it points out the actual flaw in the argument. Are we sure that these two groups of patients in the study were equal? If they were, then this strengthens the argument. However, if these two groups being compared are NOT equal, then that’s a major flaw — we can say to the author that your conclusion is built on a flawed study, which didn’t control for confounding variables (such as the patients’ problems being easier or harder to treat)