I have a 2013 Civic Si Sedan, the pop sound for me comes from the two rear windows and the from passenger window. There is no noise from the driver’s window switch. That switch is the only one that has the auto close/open feature. If you notice, the pop only occurs when you release the switch after lowering or closing the windows. Sometime the clicks are louder than usual, this suggests that there is a buildup of electricity, like a static electric buildup, which gets released when you move the switch. If you close the windows and flip the switch to try and close the window you get the pop in the speakers, whether the radio is off or not you still get a pop, the sound varies and sometimes it does not even happen.
So there has to be a discharge of from either the switch on the driver’s door or from the electric motor in the door(s). Kind of like when you turn your lights on in your house and hear a pop sometimes. Try it, slowly turn on a light, you will hear pop sound.
Back to the switches, the fact that the driver’s window switch does not pop, it’s a different switch, might mean you want to look here first. If you can remove the switch panel and try moving the switches while they are not in the door might help see if they had improper metal to metal contact or poorly isolated. Wonder if you can replace the passenger side window switch with an automatic would you get the same results.
And guess what, when i sit in the any passenger seat and lower and close the window, I am not getting a pop in the speakers. This leads me to believe that the problem lies in the switch panel on the driver’s door.
Looking further, has anyone pulled off the door panel and watched the motor in the dark when you try and lower a window? If you see a discharge of electricity and it will be quick, there is your problem. The discharge will escape and hit the frame and you will hear a pop. If you do it in the dark you will see a spark. You will need to do the same for the driver’s door switches. It might be that the window motors are not insulated well, so you have metal on metal contact and the discharge goes right into the interior door frame, or the switch in the driver’s door.
If I have time this weekend I will give it a shot. If I am right, all that needs to be done is isolate the switches from metal to metal contact.
If not then this is a characteristics of the Honda Civic SI. Sorry could not help it.