You wouldn't need time to internalize the idea that the minority is different, when those people are ACTUALLY different by virtue of being from fantasy races.
Also, you are imposing a lot of logic from our world to a fictional world with very different rules and history.
You do need to internalise it, even if they are of completely different species. Do you consider Somalians different from yourself? Do you consider Indians different? Do you consider chinese different? If not, why? There are clear physical differences between them and (at the very least me, but I'd imagine) you as well.
The reason we normally don't regard even physically different people as "not like us" is because we consider them human. And since we consider ourselves as human as well, we regard them as "part of the tribe" in a sense.
Considering the setting here, this same concept would apply, just with a different umbrella term. You'd have "humanoid" or "intelligent being" as the overarching concept, to which all fantasy beings and humans would be assigned to and only after the previously mentioned prerequisites are met, would certain species be excluded and hated as an outgroup.
As a small aside, biologically speaking, if interbreeding between the fantasy races and humans is possible, then they aren't technically seperate species. At least not completely. They would be, if I remember correctly, subspecies.
And to adress your second sentence. What are you talking about man. All fictional stories are based off the real world. We live in the confines of our own perception. We cannot create a story that has no connection to our world. Thus, we can use real world logic on it. You can ignore the logic, if you want. There is no issue with that. And you can enjoy it even if you do notice issues in logic. I still really enjoy this manga you know. I am just pinpointing misconceptions and flawed worldviews, because they slightly annoy me. Of course, what I find to be misconceptions and flawed worldviews is very biased. There is a lot I cannot see, because my bias makes me blind to them. I just want good stories with believable worldbuilding and a good depiction of how humans interact.
Ahhh, the quote I like to judge everything by is the following: "Never attribute to malice that which is adequately explained by stupidity." This is the main reason I hate when something is demonised. Be that religion, state, or in the real world billionaires, jews, I hate it. Most people are just incompetent, me included. They don't want to hurt people for the sake of hurting people. But again, that's most. There are certainly people that do that.