Generally, if touching the windings stops the noise, you can move the windings to the side a bit and that will solve the problem. If you apply anything to the windings, apply it only where necessary. Don't apply it to the entire transformer. There's a good chance that nothing needs to be done to the transformer, especially if the amp will not be installed in the passenger compartment of the vehicle.
The phase switch is used when bridging two BD amps. One amp is set to 0°. The other is set to 180°. Setting it to 180° inverts the signal.
The BD is a variation of the Class D. Most class D amps are class AD. Instead of using both positive and negative rail voltage, it uses a single rail that driven up (to act as the positive rail) or down (to act as the negative rail) as needed by the output transistors. If you really want to know more about them, read the following patent information.
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HERE.
The subsonic filter blocks inaudible frequencies so that the amp won't waste energy trying to reproduce them.