Most of that noise is from the geared Primary drive. The rest is from the gearbox. For technical reasons, Belt and chain drive (and a lot of shaft drive) bikes use straight cut gears in the primary drive and gearbox.
With geared primary, the input shaft on the gearbox turns backward (unless the engine runs backward) so there is no way to make a true direct drive gear like they can with a chain/belt primary. This means there will always be a bit of gear noise in every gear.
