I totally agree with those who suggest that the people who are judging this whining sound may simply not have hearing acuity to detect the sound which affects you. Like others said, that can be a combination of actual hearing loss, and just the dulling of perception as a result of spending a lot of time in a noisy environment. And I absolutely accept that the sound you hear may be real, and that it can have painful effects like the headache you describe.
The problem is that detecting this sound is so subjective, a result of normal variations in individual human hearing compounded by the other factors already mentioned, including gender. So I like @Triedaq’s comment about testing the alternator electronically to find out if it has an electronic defect. That would be the easy way to identify and quantify the problem. To support the evaluation, perhaps you could insist that the dealership compare the results on your car with other new cars on their lot.
Otherwise, you may need to somehow find a university sound research lab which would have equipment to actually measure the sound frequencies produced by your car, and by other new cars like yours. Presumably, that would show if yours produces a different sound signature than all the rest. My point is to find a way to eliminate the subjective aspects of detecting this problem, either electronically or with sound measurement equipment.
I empathize with you because I have better than average hearing, by which I mean that I notice sounds which others miss. So I appreciate that this can affect you painfully. I hope you are able to resolve this completely, and soon.