a stock stereo and speakers are designed to play all frequencies fairly uniform in volume over the useful frequency range of the speakers. And yes, some stock stereos do have some built-in equalization, especially the newer high-end cars.
When you change out the cd player and speakers, you will need to apply some equalization. What is happening is there are peaks and dips in your frequency response, not all music plays ALL the frequencies all the time. When it hits a dip it sounds lower, when it hits a peak it sounds louder.