This is how I could set it up:

1. Project Settings -> General -> Display -> Window -> Size: Width=64, Height=64
2. Project Settings -> General -> Display -> Window -> Stretch: Mode=viewport, Aspect=keep
3. Add OS.window_size = Vector2(640,640) to in a _ready function of your main scene.

The last step probably could be done in a more sophisticated way, though it works well like this. Result:

Exactly what I was looking for, but didn't know it. Nice :)

You can also set the Test Width/Height in Project Settings/General/Display/Window to your upscale resolution (640x640 in this example). OS.window_size would be good for in-game resolution settings though!

Great, thanks :)