If the noise goes away then sell it
It doesn't sound that bad to me but I'd agree with Greyracer that the primary gears could cause some of it. I'd bought a Raptor last year from a friend who I knew was very picky about maintenance and when I first heard it I couldn't believe the engine noise it had. Turns out he'd had a shop repair the typical 2nd gear problem on those quads and when they put it back together they swapped nuts between the clutch and crank gear shafts. They had the same threads but one needed a 27mm socket and the other a 32mm. The larger nut needed to go on the crank to cover the gear properly and since they reversed them the nut backed out to the point you could turn the gear a couple of degrees on the shaft by hand. I swapped the nuts back, installed new lock washers and 1/2 moon key and it's as quiet as new now. So if you're concerned about the noise enough to remove the top end for inspection, you could also pull the clutch case cover off and check the tightness of that nut.
Some of you are commenting you hear unusual or concerning "top end" noises. I can tell you my bone stock well maintained '07 has a pronounced lower end knock while the engine is idling. This seems to be clutch/transmission related If I pull the clutch in, the noise is minimal. My bike has been like this since it came out of the crate. This issue has been discussed commonly over the past few years.
To try and isolate "top end" vs. "bottom end" noises you can use a long screwdriver hold the screwdriver handle to your ear, and touch the blade tip to different points around the engine. You will hear noises that get louder as you pinpoint internal mechanical energy motions. The best accurate tool is an automotive stethascope, but a long screwdriver works ok also.
I put a Wiseco piston in my 426 many hours ago and it made more noise, the piston had more clearance than the stock one.
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