That kind of makes sense. The EQ part of the guide tries to get you to a "flat" frequency response. This actually sounds kind of dead but it's a great starting point for you to tweak the sound to your tastes. Once you get a good flat EQ, most people end up bumping up the bass and treble (or subtracting some midrange) to get a sound they are more used to. The metered tests are great for finding gaps in your system (where your sub only goes upto so many Hz and your front speakers cut off above that) or peaks (where you have several speakers all doing thier part to play a frequency and it gets over represented). Some cars produce their own gaps and peaks too. Once those are EQ'd out, you can then tweak the sound to ear.
I was surprised that the AutoEQ in Alpha8 sounded great (maybe a little bright) right out of the box!
I guess you had a great ear already!