Sure, and I totally get that. If my manager came to me and said I had a perma-scowl and my voice fluctuated too much in pitch, my first question would be "well, okay, but what exactly am I supposed to
do about that?" (Edit: I noticed, too, that I definitely scowled when I was thinking about that!) Granted, I don't think I'd be posing that question to my manager, but to my therapist instead.
At the same time, though, it looks like you've already experienced some consequences because of these things:
> I subsequently was not awarded a raise I was promised despite delivering on numerous advancements technologically (and monetarily), the program I was involved with was dissolved, and there was talk of reassigning me.
This is what I was talking about regarding it being a career-limiting factor, and acknowledging the situation. You can say it's bullshit all you want (and, for the record, I agree with you on that), but, in this case, you've seen first hand what can happen when you don't fit that imaginary mold. And, I would claim that, at least in this instance, it was constructively communicated to you, since you mentioned making changes and subsequently getting better results.
Whether we like it or not, people pick up on things like body language and vocal intonations. If you're lucky, not conforming to peoples' expectations there will make you seem "odd," or maybe "eccentric." If you're not, then, further down the scale of reactions you may receive could include thinking your manner of personal interaction is "weird," "unsettling," or, even "creepy." And, these are all serious problems if you ever want to hope to communicate with and be taken seriously by the majority of people.
Again, I want to reiterate that I agree with you, and this is all basically bullshit. But, like it or not, that's the game you have to play if you want to get your ideas across to people.