+1 for the reminder that in the original box it was quite clearly implied that there’s a lot of rampant mutation in the setting. Cosmetic mutations, that sort of thing. In a lot of the earlier books a lot of NPCs were noted to have strange mutations, as well. So saying that the cleansing wars were the sole/main reason for mutations in the races is a bit disingenuous.
Another thing to keep in mind is that if Athas’ star is a red giant (which, yeah, it is), that means its putting out a lot less UV radiation. Which means that’s not really a “good” source of mutation. (it also means that you’re not going to get as much sunburn, if at all, and skimpy desert attire actually makes sense, since you only need to worry about the heat from the sun, and not the sunburn from the UV radiation, but that’s another topic). As a result, the Pristine Tower makes an excellent substitution for that. The tower was last used when they trapped Rajaat and transformed Borys, but then Borys went crazy and everyone fled, and the dwarves stole the Dark Lens.
Since then, there’s probably not anyone who knows what they’re doing keeping an eye on the Tower. Sure, there are the shadow giants, but their understanding of its workings are probably somewhat limited. So the tower was probably “on” when the dwarves stole a key component, kind of breaking/short-circuiting the whole shebang. Since then, it probably emits random bursts of mutagenic radiation, explaining a lot of the “mutability” of the races.