Culture would also factor into this, so I'd say it would actually be less realistic to have no prejudices at all - for example, lets say we have two groups - group A values martial prowess and doesn't particularly care about peace, leisure time or nature - whereas group B highly values knowledge, nature, peace and leisure time but doesn't particularly care about martial prowess. I highly doubt the groups wouldn't have prejudices about each other - with members of group A seeing the majority of group B as decadent, weak whelps, and group B seeing the majority of group A as violent, ignorant barbarians.
Even if they weren't engaged in outright war, I don't believe members of either group would treat members of the other fairly - higher prices for goods, etc. - unless they proved themselves in some way to their society.
Culture would factor into this, well we are talking about culture.
If the other group *are* violent, ignorant barbarians then it is not racism as such to work on the assumption that any members of that group when they arrive will behave as such until proven otherwise. A racist however *cannot* be proven otherwise, because the racist derives the barbaric nature of the other from the appearance of the creature, meaning they simply refuse to take seriously any evidence to the contrary, clinging to their initial prejudice; the stronger the racism so to speak the more evidence is needed. For example, if we have a goblin civilization that tends to fight with a human civilization with white skins but also babysnatches from a black-skinned human civilization which has little contact with the white skinned one, the white skinned human civilization will initially treat all goblins with suspicion but also treat black-skinned humans with equal suspicion. If one of the black skinned folks was however to turns up and join one of the sites of the white-skinned civilization then we would see whether they racist or not. If they were racist they would treat such an individual with suspicion, while if they were not racist they would be fine with them once they realized that they came from the other human civilization not the goblin one.
On the prejudice side of things . . . as long as there's no absolute trends, there isn't an issue. Don't tie prejudice just to species or color. Add in all kinds of prejudiced traits, both physical and mental. And give high speakers the ability to change peoples' minds about said prejudice. It's only when you make something highly likely to happen that it becomes a problem. Heck, give these prejudices a logical underpinning, even. I'm sure the original cases of racism back when we were all primitives stemmed from competition for resources. The modern stuff came from a lot of different sources, depending on where you are. The Southern style in the states was boosted by black slaves taking over jobs that free whites were paid to do beforehand. And then further amplified on purpose by the slave owners as a way to keep the slaves from getting freed earlier.
It's a lot of work, so I don't blame Toady for not getting into it. Just, if the systems come into place for it as a natural consequence of development, think about it?
The primitives never invented racism when they fought over resources because they seldom fought people who were not closely related to themselves; everyone you are fighting looks just like you do. Racism is pretty much a modern thing entirely and has to be basically with improvements in naval technology bringing together people's who are not closely related and look different into unequal conflict. The inequality thing is basically crucial though, racism tends to be more about superiority-inferiority than friendly-hostile. The white folks become most racist when they conquer all the black folks in Africa (19th Century), because they decide they are superior and 'more advanced' than said folks. Really most racism is of the superiority-inferiority kind and totally rooted in a mixture of colonial conquest of exotic locales and the accidental correlation of blackness with slavery (so not so complicated). A more uncommon form of racism is the hostility racism, of which the only real example is antisemitism which sees the other not as stupid degenerates but as a sinister conspiring enemy with power.
The first kind is related in internal hierarchies to a society (so master-slave, conquerer-conquered) while the latter corresponds to prolonged in-group, out-group conflicts that are not able to be resolved. Both from a coding level are really matters connected to the ability of the AI to conclude information about an individual based upon secondary traits that do not in themselves inherantly imply the information being deduced.