I'm an electrical design engineer and all I can say is that the instruments we use for testing for spectral "flatness" are not the same analysis instruments that you are using when you play you equipment (your ears). The instruments help work out real problems with a design, like resonant ring, clipping, and phase problems, but the spectrum analyzers we use take a sample over time to find the amplitude of the frequency components, and I don't think that is what the ear and brain are doing. It's a different sensing and analysis method, so I can't say what I see on my analyzer is what people are hearing.
I just don't know about hearing, but the instruments are important for knocking bugs out.