I've done some more research and my opinion is somewhat similar to yours. I'm pretty positive I have a premium sound system, I'm fairly sure there is a factory amp, and I'm fairly sure that has something to do with my whining sounds.
I know next to nothing about audio so forgive me if I'm sounding like an idiot. From what I've gathered on google searches, I could have an issue with the RCA plugs that go into the back of the headunit. I think those have something to do with the factory amp. There is some grounding issue with them, or some interference issue where the RCA's are too close