Since this is a vertical engine setup there is another belt besides the PTO. It is call the drive (motion) belt. Now the two IPL for this mower does not show a Kohler being used so this might be a transplanted engine. Or simple going the layman model is pulling up the wrong IPL. This is one reason why we insist on the model from the serial number tag that in this case should start with 13 or 14.
But as you said it comes from the engine shroud area so it should not be a belt. It is one of some problems that you got take the shroud off and have a look see yourself as we can't do it for you. Could be anything rubbing on the shroud or flywheel. I have yet to see a Kohler Command with a flywheel side ball bearing. Note flywheel magnets do come loose on Kohler engines and could be causing the noise. I even seen one rubbing on the crankcase because some idiot used an impact to install the flywheel and had busted the taper mount.
As I said it one of those things you got to look for yourself.