It's a weird situation. In D&D, the gods, by default, literally exist and can even be met in person via planer travel. So the myths, or at least many of them, about them should be at least partially true. But, as you say, there are other problems with that: if you have a world where you can't meet the gods, if you don't want certain gods to exist, if you don't want the gods to have active influence in the world, or even if you don't want humanoids to ever be even "Usually Evil." So yeah, it's an unfortunate mix.