I don’t think setting the project time signature to 6/8 will set the click to dotted quarters. I’ve never been able to get that result. I would LOVE to be wrong about this!
The funny thing is I’m pretty sure you COULD do this until Cubase 8.
I remembered this: [gelöst] externe VST² - sidechain einrichten - Auf Deutsch - Steinberg Forums
and I just tried it in Cubase 7 and you could set the count base to 3/8 in Cubase 7. Might be a little programming slip, but I definitely agree with NYFC that the whole metronome could be improved.