The starter clutch is behind the flywheel, LH side cover.....the engine clutch is inside RH crankcase, but not your area of concern.
In easy to understand terms..the starter clutch allows the starter and related gears to grab the crank and rotate the engine, activated when the starter button is depressed....coupling the starter gears and crankshaft...cranking the engine over. When the starter button is released, the starter clutch disconnects itself from the crankshaft (engine now running).
So the starter clutch and engine clutch are in two different areas and hold different functions. Your only concern at the moment is the starter clutch area which lies on the backside of the flywheel....I'll submit that is where your noise is emanating from....very likely loose starter clutch bolt(s) of which there are 3, allen heads to be specific. Have loctite on hand, too.
You'll only need to pull the left hand crankcase cover....not the right.
Prior to doing this exploratory...I'd again advise researching a parts breakdown in the online fiche....
ronayers.com: Online Shopping Motorsports Parts for your year and model to familiarize yourself with what you'll be looking at.
After pulling the flywheel , you'll be looking for exploded, missing flywheel magnets (front side of flywheel, worst case scenario), loose bolts (on the backside, easiest fix), broken springs or defective rollers inside the starter clutch arrangement (may require a further parts purchase)
Just for yuks, my money is on loose bolt or bolts on the flywheel backside.
Be aware the flywheel and crank are "keyed"....there is a woodruff key coupling the 2...the flywheel pulls straight outward (thus the puller tool) and reinstalls straight inward.
I've done an EX500 flywheel pull due to extreme "clunking" during starting....in my case the starter clutch springs were fatigued....the rollers were bouncing around causing noise.
Loose bolts are very common...some youtube vids may even exist with before and after noise, too. Here's one with exploded magnets,
in the vid she pulls the flywheel using puller, all that I've mentioned are visible.