On a motorcycle, you never want the car running, as it will increase the voltage that much more, and there really is no need. Bikes, other than Guzzi’s, dont pull enough current on starting to be a problem. So essentially, you are starting from a charged battery rather than another vehicle, evan though that battery is in a car, rather than on the sidewalk.
disconnecting a battery from a running bike to switch them could cause damage, however, becasue some of the more modern voltage regs will cook when you do this. THis is true of many cars as well. I would never do this, unless I was very familiar with the electronics of the bike in question.
Most noise that would be generated by applying the jumper cables to the battery would be obsorbed by it, the dead battery acting as a big filter capacitor, so I doubt it would cause any problems, but my expertise is with older bikes, and YMMV. When I worked as a bike wrench, it was on old brit bikes, harleys, and a few jap bikes, guzzis and beemers, but even so that was a decade ago. My sepcialty was motorcycle electrics, and electronic engineering was my major before I dropped out to become a rock star(that worked out so well for me)…