The reason that a lot of other console developers need everything to sell millions of copies is that to make HD, polygonal games, you need to have legions of employees that you're paying for months and months.
Have you seen Atlus games? Aside from Catherine, they've basically never had to make anything with more advanced graphics than a PS2 game. So they're saving a fortune on artists, and I assume their development costs are much lower than some other developers, because keep in mind that even selling in the high hundred thousands may work out to a profit if their development costs were only a few million.
In particular, I assume stuff like Etrian Odyssey, a dungeon crawler with 2D sprites with next to no animation (plus it gets away with recycling environment art a lot because it's a dungeon crawler) must have relatively low budget. They jump right into development because they don't exactly reinvent the wheel each time, bang out some art, then boom, dungeon crawler fans buy zillions of copies of this game that cost them probably little time and money, relative to other projects.
They probably do take a loss on some projects, but keep in mind they've been reissuing/porting the fuck out of Persona 3 and 4 (and the earlier ones to a lesser extent), and those probably sell like gangbusters, with fairly minimal time and money.
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