Every sound is made up of a fundamental (its actual pitch) and many overtones, which are higher-pitched components of the sound. It is in part the mix of overtones -- which overtones are more prominent and which are more subdued or not even audible at all -- that makes a sound "bright" or "dark". When you turn the tone knob on an amp clockwise, you get a brighter sound (the high components of the sound are emphasized); when you turn it counter-clockwise, the low components are emphasized.
You can use your embouchure like a tone knob, changing a shakuhachi sound by adjusting the overtones, emphasizing some, de-emphasizing others. Emphasize the highs and you get a bright sound; de-emphasize the highs and you get a dark sound. Of course different shakuhachi may be inherently brighter or darker, but you have a great deal of control over the timbre of individual sounds.
A kari position helps to make the tone bright (a meri note is always darker), but the timbre is also affected by the exact shape of your mouth.
Ro buki -- repeatedly blowing Ro -- is a great way to practice using your embouchure to adjust the tone or timbre of a note. Ro is a note that you can't make loud just by blowing harder -- it jumps very easily to the second octave if you simply blast it with breath. So you make it sound louder by adjusting the overtones with your embouchure -- going for that "honking" or "trumpet" tone by emphasizing overtones in the 500 - 1000 Hz range. Once you have the feeling of making this adjustment to Ro, going back and forth easily between "simple tone" and "trumpet tone," you can easily apply the same technique to other notes, making them brighter or darker.