How many miles are on your engine / drive train?
That bulletin applies to 07 models and mentions 06s. His scoot is an older Evo.
My 98 Evo 1340 doesn't make this sound, but it makes others I consider to be odd. I know the source of every odd noise and know the ramifications of ignoring them.
If I had a clunk like that goin on, I'd definitely pull the primary cover, drop the plug wires to keep the bike from starting) and hit the starter button to locate the source of that noise.
Things that come immediately to mind: Compensator sprocket, loose chain, starter issues. It would be a bad thing for any of these to get much worse and leave your stranded somewhere and damage your bike. A comp sprocket issue could take out your crankshaft, requiring a complete teardown and lots of cash to fix.
And of course, it could be nothing to worry about.
But I'd sure want to know if it were my scoot.