@Yamibi
I actually still don't get how you think the protagonist is being racist. Let's go through your argument point by point.
1) "treats this female with so much reserve, never belives in her stories."
- Would you believe her if you're not into mangas and animes? It's a normal reaction by people who doesn't dwell in fantasies. In comparison, you can see his ex-gf believing her from the very start.
2) "MC calls for authorities right away and even not informed her about it."
- That's actually what every law-abiding citizen is supposed to do. You have a girl who claim she's a knight (possible mental institute patient), has no identification (probably illegal immigrant) and claims arrived via magic (possibly dangerous person). I know many mangas downplay this as if it's normal to meet strange people, but that's not what you're supposed to do. If something goes wrong, you will be held responsible and may be punished to the full extent of the law that governs that offense.
3) "From this last conversation with his ex seems like he wanted some kind of compensation for keeping her"
- It's not that he wants compensation. He deserves compensation, because the government (his ex) told him he can't meet anyone, he can't sell his produce to anyone and he can't leave his farm. When the government imposes such restrictions that causes the individual to lose their income, the government must compensate them for their loss.
4) "He is never fully truthfull with her, does a lot behind her back. "
- He thinks of her as a kid. As a parent, do you always tell the truth and nothing but the truth to kids?
5) "There is also a scene in previous chapter when he shows map of Europe and says that people like her live there."
- Because she looks like European. It's not wrong that if she goes to Europe, she will meet more people like her. She herself misunderstood him to be a slave trader when he showed her pictures of Europeans who look like her people.
6) "Whats more when you think how japanese people treat westerners: they are open to visitors but if you try to live there you would meet with a lot of racist comments and behaviours."
- Which country isn't racist to foreigners? Name me one. Just one. Certainly not America. America is racist to their own people.
7) "There are many places in Japan that won't accept non-japanese people (hotels, restaurants etc). "
- When foreigners go into their restaurants talking loudly, throwing food around, complaining loudly about the food or the waitress's bum or whatnots or generally disrespectful of local customs, can you blame the Japanese? This happens very often, even to this day. There are signboards stating 'Japanese-only', yes, I admit those exist, but they aren't actually enforced. My Chinese friends who speak Japanese often dined in restaurants labelled 'Japanese only'.
You can blame a lot of recent Japanese prejudice against foreigners to one guy, Debito Arudou (David Christopher Schofill), an American who managed to become Japanese due to marriage and then ruined everything up for everyone by suing everyone.