Replying to @wessexweather@mastodonapp.uk
@wessexweather @openvibe
Ok so I had to pursue this, and I went to the actual WMO manual (link below). The documentation does not explicitly say to ignore transparent cloud, and it DOES say to count all cloud.
So from this I would conclude that you do count oktas of transparent clouds.
Relevant paragraphs: 15.1.4.1 and 15.2.2