I see. Thanks for the help on this. I am going to stick to 2D pixel games for now until I figured out upscale those games to 720p. YouTube truly is a tricky encoder to work with.
Edit: I do make things complicated for myself. I know there is simple solution but I am not aware of it or I do not want to be aware of it. I will try to ask more questions about this in the future if I encounter problems.