Not as confused as I am when it comes to technicalities of notation! I was starting to have doubts, but it turns out that the Dancing Master edition of 1698 has the tune in 3/9, so there is no typo involved.

You can see Roger of Coverly on page 167 at http://memory.loc.gov/cgi-bin/ampage?collId=musdi&fileName=004/musdi004.db&recNum=174. The default images aren't too easy to read, but there are 300 dpi tiff versions available which are easily legible.