I am not sure about your first 3 points, but in the Descendant Chart Options window, you can click the Title tab and then delete the title. I just tried it and the title disappears but leaves an ambiguous black box in its place.
I changed the top margin in Layout from .500 to 2.500, and it definitely increased the top margin. I am not sure why this would not be the case for you.
I checked the results of changes using the Preview.