I'm pretty sure every one of those games except Papers, Please and Hotline Miami, and maybe even those because I don't know much about HaXe or Game Maker, is made with a 3D engine (Unity, XNA/MonoGame, whatever). I mean, you namedrop Sunless Sea, but they do an absolute ton with 3D effects to create the desired look of the game.
Yes, they're made with a 3D engine because the platforms and the widely available frameworks are all 3D. However, the games themselves, the gameplay, and the primary aesthetics of the games are not 3D and would be just as home in a 2D or 2.5D engine and hardware with at most minor changes to the visual look and feel of the game.
These games are fully 3d modeled and in no way a 2d game. Their gameplay may be portable to a 2d platform, but they are not 2d. The is a significant difference in terms of development.
