I'm in two minds about this.
Initially, I was thinking that xenophobes shouldn't hate their own subspecies at all. Especially when those subspecies are, for example, exactly the same as the old species, but with the "Weak" trait replaced with "Very Strong".
This is less a case of "Eww, foreigners" and more a case of "Rejoice, bretheren, for the promised Ubermensch is here!"
But then it occurred to me that if you've got an ocean-preference base species, and then you GM yourself a desert-preference version for colonisation purposes, I think it would be entirely reasonable for the two groups to dislike each other. One reviled as a bunch of bottom-feeding atavists stuck in the past, and the other as a bunch of freakish Frankenstein-experiment extraterrestrial sand people quasi-xenos.
So I really don't know a way out of this that wouldn't cause exactly as much flavour-harm as it fixes.