i don't know a whle lot about it, but when you pluck an open E, the E is the fundamental tone, however there are a lot of other frequencies going on, like you said, in the rest of the frequency spectrum, so an EQ accentuates certain frequencies over the rest, so that say you play an open E with the hi-mid turned up, the frequency 1.6kHz is boosted. When the E is plucked, you still hear the fundamental E, but you also hear the 1.6Khz brought out, so it will sound a little more hi-middy
that may not be the best way to explain it, but it's the best way i can think of saying it--either way, your EQ is just fine. These amp businesses hire a special group of people (R&D) to find what the most effective EQ points are for bass players, and put those on because more people want simplicity. 3-6 knobs are better than 100 knobs for the majority. If you feel that you don't have enough control over the frequency spectrum, i'd suggest into looking at a 31 band graphic EQ, or a parametric EQ.