You really need to tell us a bit more such as age and mileage of your XT6E. What's it's history in respect of use (used off-road or looked after etc).
I'm no mechanic BUT for what it's worth - both my XT's have a few quirks like this. No one bike is exactly the same as another.
I have always found ALL large capacity single cylinder motorcycles suffer from vibration and this can often lead to odd, bizarre and mysterious noises originating from the engine.
Something silly like a worn sprocket or slack chain can cause odd noises.
You mention the clutch - the noise might originate from a worn or badly adjusted clutch
I suppose if your bike appears normal in every other respect and is reliable - who cares about a few odd (unexplained) noises.
The XT engine is bulletproof reliable and is famous for it's ability to operate without being properly serviced and looked after. It just keeps running until it finally goes BANG!
I think I would start by giving the bike a FULL service (including checking tightness of all fasteners etc.). If the noise persists, you should take it to a trusted workshop / home XT expert for diagnosis.
It is probably a badly adjusted clutch.
Triumph Bonneville 800 (2004), Yamaha XT600E (1999), Honda XBR500 (1986).