Whether the two kinds of therapists use the same techniques is irrelevant. The conclusion is about which therapists are more effective, not which forms of therapy are more effective, and (A) doesn't change the fact that patients referred to the new therapists made more progress.

The author draws a conclusion based on samples that probably aren't representative. He ignores the possibility that patients referred to therapists using the new therapy are just easier to treat, and their improvement could be due to that rather than to the therapists themselves.

The author doesn’t assume that this. Instead, his conclusion is about therapists who practice traditional forms rather than the new form. Those therapists may still be trained in the new form and simply choose not to practice it.

Even if therapists practicing the new form of therapy are significantly different from those practicing traditional forms, this doesn’t change the fact that their patients made more progress. It also doesn’t weaken the conclusion that these therapists are more effective.

The author never assumes that rapport doesn’t influence therapists’ effectiveness. Even if he did assume this, it wouldn’t impact the conclusion that the therapists practicing the new form are more effective because their patients made more progress.