So I got a new update for Godot Super Scaling, which greatly improved the image clarity. This separates the upscaling from the super sampling in 2 passes, gaining quality and a better image. At normal settings (like 90% to 110%) it looks the same, but maybe slightly better. At higher scales (like 150%) it actually looks slightly worse, but I would recommend no one go that high anyway and most people don't have the rigs. However, at lower scales it looks substantially better.
This is the new version at 1080p native:

New version 540p upscaled to 1080p:

Old version 450p upscaled to 900p:

You can see the old version was very blurry in comparison, but that was the limitation of the original method I was using. With the new method, there are 3 viewports (the real screen viewport, then the upscaled viewport, and then the super sampling viewport). So it is a chain, kind of a hack since Godot does not have real multi pass support, but whatever, it works.
Release live on Github now.
https://github.com/cybereality/godot-super-scaling/releases/tag/v1.1.0