Yes you idle the bike until the fan kicks without touching the throttle while it does it, it should be done when engine is initially cold, not certain where you read the 1200gs process but I think you will find there will be differences in the 1200GS process according to the year model/BMS fitted
In terms of documentation of the 650GS process the GS911 software tells you what to do, beyond that the US Dealer TSB's which have paragraphs explaining the procedure have been available over at f650.com in the FAQ for many years
There have been urban myths develop over what constitutes BMS reset procedures etc on the 650 and other models, they in part came about due to people (including a few dealer techs) applying procedures from old models to the new models instead of reading the manuals