You're right, the doc is not up to date, my bad.
The recommendation is to use the latest stable version, aka Eclipse Luna SR2.
And earlier Milestone version of Eclipse Mars is also used by many, and seems to be working ok. But it's more being "on the edge", so I'd recommend staying with Eclipse Luna. I'll update the documentation ASAP.
The Standalone version of Counterclockwise enables updating the counterclockwise plugin easily.
What still remains to do is being able to change the underlying Eclipse platform of the Standalone version (for instance start basing it on Eclipse Mars instead of Eclipse Luna) without requiring users to re-download the whole standalone version. So once a year, as is required for Eclipse itself, by the way.
Hope this helps,