I agree with the first part but the second doesn't really follow. How will your belief that phrenology doesn't work influence the result of such a test (assuming you live in a world where such tests are even considered)?

Phrenology doesn't allow the same "luxuries" as the polygraph because people are more or less stuck with the size and shape of their skull. Their guilt is exclusively in a chart not in their beliefs. Only thing that matters is if the people (judicial system) giving the test believe in it.