There is a lot of conjecture on the cause but wide agreement on the effect, the noise is just noise. It doesn't cause any harm. It seems to have started with the 2007 model. My 2007 started making the noise after the first oil change. It has well over 100,000 miles now and is on its second owner. I probably have it on my 2012, but haven't really paid attention to noise changes. I think I'd notice something if it developed something actually serious like a con rod bearing knock.
I *thinK* you're referring to something commonly called "idle knock". I think...
The 1000's are well know for this, it's discussed at length on their board. That is, idle knock a not too common occurance for a 1000, seems to appear (if it is going to appear) somewhere shortly after the first oil change. It strikes random examples of the cycle, not every cycle exhibits. On that cycle, it appears to be mechanical stack up of clearances (of various mechanical components) that is the primary cause, as documented extensively by the fellow who developed a fix (yeah, and just try to get one, they're scarce, and lengthy backorder).
Anyway, that's the short history for the 1000's, from about 2007 thru present 2015's (the motor re-design did not change or affect the clearance stackup of the related components).
However, I thnk these are the first reports that I have read of idle knock on a 650 model, *if* thats what this is.
Myself, I was going with cam chain rattle.