Another notable, if old, train simulator from Japan is OpenBVE. It was easy to model railroads on it. Many short Brazilian routes were/are modeled in OpenBVE. It is particularly convincing since it simulates well the typical lateral wobbling that metric trains are known for.
openBVE's not directly Japanese, it's an open-source re-implementation of the original BVE 2 and 4, which is.
Do you mean actual Brazilian railway track engineers used this game to plan/develop actual routes? Or just that you can play Brazilian routes in the game?
Just to play the routes.