Charging a battery involves chemical reactions, doesn't it? Without passing judgment on whether what the OP experiences is "real" or not, it seems to me not impossible that either heat or a reaction that's happening during charging/use (not that these are mutually exclusive) might be generating some compound that's causing the OP's symptoms. I don't have the time to Google battery-charging chemical emissions right now.
OP, you can do a blind test in your home, if you get someone to help you. Be sure to expose yourself to more than two devices, and also to expose yourself to the MBP in all its states (charging/off, charging/on, off with charger not present, on with charger present and connected to mains but not to MBP), and do some experimenting first so that the sound of the device or its position in relation to you isn't giving it away.
It's absolutely in your interest to make sure the blind test really is blind, or you'll never get an answer. Remember, a blind test isn't an insult.