Whoa. The Tsukinos are even richer than I thought.

[Bob Schroeck]

And Makoto has her own place with no visible income or visible family at all.

Based on some of the research I've done, I'm working on the assumption that she has a lot of money from compensation payments for the deaths of her parents, as well as payouts from whatever insurance they had.  Given the historical context, the plane crash in which they died was almost certainly Japan Airlines Flight 123 or an analogue thereof.  According to multiple sources I've checked (and don't take every detail in that Wikipedia article as gospel, because it's subject to edit-warring that keeps shifting the blame and changing the story), Boeing made compensatory payments to the families of the victims that have been described as "healthy" and "generous", and JAL itself paid "condolence money" without admitting liability; there were also lawsuits filed in the United States, the results of which I have yet to actually discover. 

Given all that, and what her apartment looks like (large, comfortable), I'm pretty confident that she's quite well off.

She almost certainly has an absentee guardian; her lifestyle is unusual but not impossible under Japanese law.

Oh, and chapter three shows some of the solution I came up with to these questions.