It was the Microsoft’s official Python extension, as far as I recall. It was possible to use some other extension for typechecking but there were some other issues with it. (Now everything works perfectly in Neovim, and my setup respects to only use typing stubs I specify in the project.)

The Microsoft official Python extension uses Pylance, which is a closed-source extension of Pyright with additional features such as built-in type stubs. This is probably what you saw.