I lost a little in translation… were you seeing color shifts with command-line ffmpeg as well, or only Shotcut presets?
I just did a round of tests using the same color you did using ffmpeg:
ffmpeg -f image2 -s 720x480 -r 29.97 -i "016,180,016.png" -pix_fmt yuv420p -color_range mpeg -c:v ffv1 yuv420p-mpeg.ffv1.avi
I changed -c:v to be HuffYUV, UtVideo, FFV1, and ProRes (and yes some complained that yuv420p was incompatible). I played back their outputted videos with MPC-BE media player on Windows 10, did a screen capture, and eye-dropped the frame to get the RGB. On every codec, the RGB values were within 1. This was true for -color_range of JPEG or MPEG.
I got confused because you ended up with x264 CRF 0. I thought the Shotcut color shifts didn’t bother you because you used scripts, but if you used scripts, then HuffYUV would still be a candidate and you wouldn’t need x264 CRF 0 … so I got confused.
If your ffmpeg is shifting colors, two thoughts come to mind. One is that your ffmpeg is fine and it’s a media player that doesn’t know how to do MPEG/JPEG color range conversion correctly. MPC-BE does. The second option could be an old ffmpeg. I’m using 4.0.2 and get no shifts with the lossless codecs.
Having said that, you’ll probably get better compression with x264 CRF 0 so maybe that’s still a good deal. 