Well for my Godot pixel projects there's a few settings I set. In Project Settings -> Display -> Window, I'm sure you set Viewport width & height. But you should also set Stretch settings. Mode should be set to viewport and Scale Mode should be set to Integer.
I'm not the best at explaining it, hovering over the settings will explain it a bit better. Viewport mode is basically like, what if you processed the space, upscaled it, then rendered. Disabled & Canvas Items modes are basically what if you scaled up the space first, processed it, and then rendered. This means that things that use scalable graphics process at a higher resolution, such as text outlines or your fade out circle or your mine cart squashing and stretching. That last thing is also why scale mode should be set to integer to avoid some oddness too.
Hopefully that helps! You may need to make adjustments to a number of things though to make it work. Like you might still have some additional colors due to the way your fade out works.