You're wrong. There is a radical difference between the advancement of your society, and essentially a fascist racist splinter group. Cerberus isn't the legitimate government of the Alliance. They aren't leaders. They aren't the government. They're a fascist splinter group. They aren't bound by laws, or any kind of social bond in conducting their experiments.
And we are absolutely talking about racism moreso than we are about patriotism. This isn't about protecting your society - this is about creating a racially pure society. Cerberus, for example, wouldn't tolerate non-human citizens of the Systems Alliance based on their ideology.
Are there any non-human citizens of the Systems Alliance? I don't recall any. Nations in ME are monolithic in terms of species. As for Cerberus not being leaders or the government, true, but that affects only their legitimacy, not the question of whether their goals - as opposed to their methods - can legitimately be described as evil.
There's a real argument about whether or not there's a difference between "species" and "race" (in the way we use it IRL, i.e., totally superficial phenotype differences). It's still ultimately an idea about racial essentialism - that being human is about some particular series or combinations of traits, not a shared culture or system of values.
Well...essentialism may be wrong in the case of human races, but true if you compare one species with another. Our brains are surprisingly plastic, but there are things we're wired for we can't escape. Even the statement "there is no meaningful difference between human ethnicities" is wrong in this absolute sense. There are no differences that could rationally justify treating ethnicities differently in terms of abilities and political rights, but clinical studies about certain medical conditions have to take ethnicity into consideration, even though even there, the difference is statistical rather than deterministic.
In the case of different species, there probably are meaningful differences that affect implementation of values through laws, since I find it implausible that there are no systematic, biology-driven differences in
life-history characteristics between species. For instance, I'd expect a species like the krogan - before the genophage - to value the life of an individual child lesser than a human would, based on the fact that they could have several thousand children per mother. To such a culture, our idea of an absolute right to life of any child after it's born would seem, and be, nonsensical.
This means that for instance, a statement like "we don't want any krogan in the vicinity", expressed by a human community, sounds rather understandable to me, while "we don't want any <insert human nationality or ethnicity>" doesn't.