Must be mechanical. Somewhere between the crankshaft, and the clutch plates. Zones no dealership is going to want to delve into on their dime any time soon.
Mine is a 2013 with the liquid cooled engine. I also owned a 1994 1100GS. When I sold it it had over 150 000 km and didn’t have any buzzy vibrations. Don’t ride the S1000XR prior to 2019. I know mates who have bought and sold in the first year due to the buzz in the handlebars and foot pegs.