You're confusing the difference between phenotype and genotype. Genotype is the species, ie Xindi. Phenotype is the differing genetics that create all the divergent sub-species, all of which are still identifiable as Xindi.^Even if they weren't, I would suspect that the differences between arthopodoid and mammalian phenotypes would be somewhat more than skin deep.
Exactly. We're talking about fundamentally different biologies here, not just differences in skin color or nose size.
It's like the Humans and the Neyel from the Sundered/Red King. Genetically human, phenotypically different, look completely different, have prehensile tails etc...two different species but still genetically human.