Well..first...current doesn't flow because "current" means charge is flowing.
The noise is a function of differences in potential (electric fields) and currents (magnetic fields). If you can turn off voltages and currents, the electromagnetic fields are reduced, and so is the noise.
There's also likely some electromechanical noise from the transformer windings humming and if you can turn off a couple of the windings, that noise will get reduced too.
Incidentally, on my Onk, the engineers spent what appears to be a ton of effort on reducing this transformer, and in general, chassis noise. It's a design consideration that often gets ignored. When things are vibrating, and those things enclose charge, stray electromagnetic fields will be created.