I haven't used the Yamalube in the rear either till the new bike, and never had a problem in the 2012. I also know that our dealer doesn't use Yamalube.
Now with the 2014, I'm using Yamalube only because I have an extended warranty, per change it's relatively cheap, and we've had a number of people who have had seals leak back there.
As Mark wrote, Yamaha buys in enough bulk that they very well may call for additives which affect the seals and it only takes them a quick simple lab test to know what lube has been used. On a related note, for a car or bike with a variable speed transmission, using the specified lubricant can be critical.