You can use OS.window_size = Vector2(512, 512) in the _ready function of your main scene to force the window to change its size, if you combine that with a preset size of 64 by 64 in the project settings, you can have a 64x64 game stretched and ready for hi-dpi modern screens :). Be sure to use the setting stretch: viewport as Callum John explained.
Viewing post in How to Set Up Godot for LOWREZJAM
I've been using a very similar method to upscale the window, but I've found just altering the window size causes the window to become off-center, which could cause it to become lost on some screens. To combat this, I also alter its position as well:
OS.window_position = (OS.get_screen_size() / 2.0) - (OS.window_size / 2.0)
Which should put the window in the middle of the primary display every time. There's a slight flicker when the game starts up, but it's barely noticeable.