Well first off - Agimori are not black. They're a dark brown skin. I think it's important to remember that in Glorantha, because in this setting if you say someone is black ,that means they actually have black skin. And if they're white, that means they are literally white. And so on.
Now, as for the topic of physical appearance (skin color in particular) relating to runes, it exists, though it's not entirely that simple. The Vingkotlings, for example, were originally Blue skinned. Orlanth was blue, so was his son, and from there so were his children. Except most of his children were not divine, so they lost the blueness of their skin, becoming a sort of neutral shade of brown. So they countered that by marking their bodies with blue tattoos, in order to emulate their divine ancestors.
People strong in the Earth tend to have a pale green skin, the color of oxidized copper. The rest are usually, again, just a neutral shade of brown.
Fire/Sky people who are close to that element (see - Dara Happan noblemen) tend to have golden-looking skin (not yellow, it's important to note. Golden), light hair and light eyes. The further removed you are from it, the more your skin looks like a dirty yellow color instead.
Darkness people (trolls, that is), have skins that are various shades of black or grey. Some have tints of blue, purple or brown in them, but ultimately it's just grey-ish.
Water is associated with blue, and to a lesser extend, green (though a more turquoise shade of the color, not like the coppery one of Earth). See the Waertagi as an example of people who's appearance is strongly connected with the Water rune.
Mind you, this is relevant mostly around central Genertela. With the Brithini and the ancient peoples of Law, your skin color is directly related to your Caste. So your first child is born brown or gray, the second one is Red (or more likely a sort of pink), your third one is golden-skinned (see above) and your fourth one is Blue. Obviously, as modern day Malkioni have drifted away from the strict practices of their ancestors, to the point where they even age and die, these colors tend to be muted or entirely lost....with people being, you guessed it, a neutral shade of brown. More devout/Lawful Malkioni might still develop a tint of color though, which is probably going to be seen as a very important thing for an individual.
Then we also get into the various other peoples, like the colorful people from Teleos, who seem to be that colorful because of some kind of a curse that Harrek breaks by stealing the Emerald Frog.
Now, the final question might be - just why is it then that everyone, when not strongly associated with a particular color, tends to default to "sort of brown"? Well, there are probably lots of explanations. The obvious ones are being sunburned from staying outside too long, the fact that the Earth is, in many ways, the Mother of All so everyone defaults to brown because of it, and so on. The Out Of Setting reason, I theorize, is that simply put Glorantha is evocative of the cultures and peoples of the ancient Mediterranean and Middle East. and those people tended to be sort of brown, so everyone in Glorantha is as well.