No, regular alien minds, for all we know the default stance should be zero care about any kind of genocide, or civillian bombardment, and only xenophiles or fanatic xenophiles would get any reletions hit from those.
I mean, it makes sense, if they have zero xenophilia, the act of killing xenos should be irrelevant to them, thinking otherwise is just applying human standards as the baseline, which shouldn't be applied to truly alien species.
An alien species without any xenophilia would probably get a much bigger relation impact from having a neighbor with a very powerful, menacing fleet, than killing random aliens they don't care about in some distant planet a long time ago.
Plus the default alien cohabitation should probably be impossible too, unless species were specifically made to be adaptable in the same enviroment, with the same kind of mindset, it shouldn't even be possible for them to survive within the same society, even if you're a xenophile, but the default human mindset just thinks of aliens as humans from a different country.
Want to create a tolerant empire where all species are equal and work together for a bright future? To achieve this ideal, almost utopian state you need to: 1. Not be genocidal 2. Set the highest laws for everyone as default 3. ... The easiest...
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Even humanity, or at least 99.99% of it, could not tolerate the idea EVER being possible to live with a good portion of the alien portraits in the galaxy, just by nature of how they look and what it seems like they do.
The devs know this, this is why they made the Blorg as a joke empire a long time ago during their streams, about a repulsive fungus nobody could possibly be able to get along with, even though they really are friendly.
This is also the default, logical stance of many other games like Galciv or Distant Worlds as similar minds, similar species, can often tolerate one another, or even like them, the bugs can understand the mind of other bugs, and they can live together, but every other species hate them and trying to assimilate them in other empires lead to terrible issues, rebellions, and unhappiness, many species are simply unable to get along, but Stellaris doesn't model that, at all.
They've sort of added it as an option with Selective Kinship but honestly, that should be the default stance for every specieis in the galaxy, and traits like repulsive should also make you hated by your own species type, we shouldn't have to waste a civic for the obvious natural stance, just to get a "debuff" with certain species, instead, thre should be an exceptional civic for xenophiles that reduces the debuff from other species, justifying taking that civic.
Something like the Asari from ME that probably use deceiving psionic tricks to look similar to the species of the beholder.