ffmpeg scale and overlay then output yuv got corrupted video
I suspect this has to do with lack 1-1 correspondence between the frame timings in the color and video, but in any case, you can just run

ffmpeg -y -hide_banner -i 1.webm
       -vf "scale=w=640:h=480:force_original_aspect_ratio=decrease,
            pad=640:480:(ow-iw)/2:(oh-ih)/2"
       -an -f rawvideo -pix_fmt yuv420p 1.yuv