Oh look, another one of those "where the hell are child protection services at?" kind of story. One child is living alone 24/7 without any adult supervision while another is literally abandoned by her parents and homeless. Is this just bad writing or is this the norm in Japland?
It's a norm in manga. After all, making a super complex backstory with full on logical explanation will be boring for your typical 'shonens', waste of budget (drawing and all that) and adds nothing to the story (except for people like us who want some reality sprinkled in).
I can't speak about the abandoned girl.
But I grew up in one of SEA countries.
When I was in high school, I went to one of the best school in the country. In my case, I just had to commute daily because I lived in the next town.
But there were many students from different cities that came to my high school, and they pretty much lived 24/7 by themselves. They rented a room/apartment near the school. Most of them were quite the responsible kids.
So, to me a story where a student from rural city moves and lives alone in Tokyo is believable.