for me--at least--these two are what keeps it from making 'good guys' level. It's probably morally natural unless enforced rather draconically. But its certainty not good.
On the other hand, pacificist xenophobia where you are like 'you guys stay out there, we will stay in here.' but you don't go full isolationist is also natural. And might even make low key good if you are active in making the galaxy a better place.
Yes, because that isn't evil or anything. And has worked so well in the modern world. As an American I'm offended you are labeling this as 'not evil.' Just saying.
Xenophobia isn't evil
in the context of the stellaris universe, given the number of purifiers and crazy televangelist empires running around. The only reason I'd say xenophobia is 'clearly evil' is that it unlocks slavery--much like authoritarian ethics--but that in and of itself isn't required. I think this would be much better recognized if slavery wasn't default for non-fanatic xenophobia. and if more AI xenophobe empires weren't slavers.