Pretty sure that this is either a bug or the result of gen-modding. AFAIK humans are a special case in that COM and UNE are hardcoded to start with exactly the same species. So even if you'd start as COM and give your race different traits than the standard humans have, the humans of UNE (which is forced to spawn when you play COM) would have the same traits and count as the same species.
In regards to playing the same species as a Fanatical Purifier, the only way I can see this working if you end up CREATING the FP in the first place -> be a fanatic xenophobe and militarist/collectivist empire and liberate a planet with your species on it.