Hehe...the name Kromagg first appeared on screen in season two's "Invasion". If you look closely, there is graffiti on the amusement park earth that says "Kromagg". All mentions of the ape-men in the "Invasion" script were also spelled "Kromagg".
As for their origins, the name is somewhat misleading. Arturo tried to explain it in the episode by relating the anthropological theory of the "killer ape," but some more elaboration was needed for complete clarity. This "killer ape" theory of evolution was an attempt to explain why some people are born murderers and why the rest of us are generally peaceful and cooperative. The theory began as a statement that some of man evolved from a group of killer apes...while the rest (and majority) of man evolved from the more peaceful and cooperative apes.
In the 60's and 70's, this theory was called into question as more and more fossil evidence began to suggest that the killer apes dwindled and died out...while our direct ancestors (the ones who would become Cro-magnon, etc.) were all appearing to be the surviving cooperative kind.
The Kromaggs come into this as an alternate history. An alternate history where the residents of earth evolved mostly or entirely from the theorized killer ape. So in reality, their alternate history comes from before the Cro-Magnon stages of man.
As for why they would end up with the name Kromagg, there is a myraid of possible explanations. The history of language and word usage could split off at several, several points during history; and the use of the word Kromagg to describe a race is just as rational as applying the word human when you get down to it. The words we choose just depends on what the originator chose and what subsequent generations took up as their own. Sometimes this can even arise from derogatory comments by outside people. A prime example is the story of Thomas J. Crapper (a real man). The first to market the flushable toilet, Crapper placed his name on the back of the tank as a poorly planned marketing strategy. Of course, it was not long before everyone began to call the fixture by the name it had printed on it..."The Crapper". It would not be long after that when many would shorten the term to "C r a p" and apply it to other things.
Tf
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