It's all about the arrangements, If you play a root and nearest minor third at the same time, they will clash if it's played too low. All you do is make the minor third an octave higher, and keep the root note the same. Unless played high up a root and major third will sound cr@p, unless it's very clean sounding, with no od/dist/fuzz. It will sound good if one guitarist has a motherbucker and the other a single coild pickup, the contrast creates a better sound when mixed together.