I had the exact same problem with the Honeywell gas control. Having called Rheem tech support, one Rep. told me there was too much gas pressure and to call my gas company. Sure, like everyone on the street has the same problem. I called back a few more times and was sent (in total) two more controls and the burner assembly. Replacing the gas control did nothing as the tone was still being generated. It sounds like an electronic alarm tone by comparison.
To find out what exactly was causing the "tone", I extended my gas line so I had a place to set up a temporary second control, pilot line, and burner that was external, i.e., not associated with a water tank. I opened the plastic housing of the gas control and removed the electronic circuit board so there were no pressure or temperature readings. The bare-bones control was then 100% manually operated.
What was discovered: The source of the noise is coming from the pilot light valve inside the control. When you press the igniter button to send a spark, the mechanical shock wave travels through the metal and into the valve causing it to oscillate and generate the tone. To prove this on the temporary rig, I would press the button to allow gas to enter the pilot tubing and then light it with a match. Also, I took an igniter from one of my spare units and connected it to the temporary rig so it was not mechanically attached. When using either method to light the pilot, there was no tone and no valve oscillation. To even further verify my findings, I went to my installed hot water tank and disconnected the igniter wire and connected the spare. The igniter was then operated external to the water tank. Again with no mechanical shock, the valve remained quiet while in operation. Interestingly enough, the gas pipe going into the control could be tapped with a wrench and the oscillation & tone would start. The only way to stop the tone is to set the dial to OFF to cut off the pilot supply. One can only conclude that gas traveling through the pilot valve in conjunction with the shock wave produced when pressing the igniter sets up a valve oscillation thus causing the tone.
My final opinion is that these gas controls are either poorly designed or defective and no one wants to admit there is an ongoing problem.