I'm not sure if Godot allows you to add extra code for your game, but you can definitely add some CSS to the html file to fix this issue. If you're interested in fixing this I would love to explain how I did it in my game. Although I didn't use Godot the principal stays the same.
You will first have to build your project without scaling at 84x48 pixels.
Then you will need to open the index.html. Inside you should see a <style> tag somewhere. Inside that tag there should be a line that says: #canvas {
...
}
Add the following code inside the canvas.
transform: scale(10, 10);
transform-origin: top left;
image-rendering: pixelated;
And that should do the trick. If there it doesn't work then send me a screenshot and I will check it out.