Very Useful thread. My 2012 FLHXSE3 has been making noise similar to the description here, clattering with the clutch disengaged, noticeable when engine is hot. I took it to the local dealer once and of course it didn't make any noise when I got it there. After a ~70 mile ride this week it was clattering quite noticeably when I got it home. I've only got about 470 miles on it.
I had the same with my 08 Fatboy Custom, rattle in the primary, had we worried for a little while, so went to a dealer and explained what was going on, he got his stethascope out and had a listen and said sounds alright but would hurt to have a look at whats going on, also told me to twist the throttle (ride a bit harder) a bit so the tensioner would take up slack when primary chain is under load. Quietened it down a little.
Got a 2012 SG as well and put it in first gear, gear clunked in really hard and then I had a rattle sound in the primary when in neutral, pull clutch in and no rattle, so I went for a ride and nothing unusual, all was OK, got home and wasn't as bad although still a little rattle.
So I am thinking along the same lines it is the chain tension causing the rattle.