Study author here. For Y-SSIM and IW-SSIM we convert the images to grayscale (MATLAB 'rgb2gray') before running the scoring algorithms. We aren't running the algorithms on luma planes. See published code and methodology.
If you use a greyscale/luma-only metric, you have to encode greyscale from the start, not convert a color image after encoding. Otherwise you're measuring chroma bit cost, but not chroma distortion. Thus, invalid.
Actually, is PSNR-HVS-M greyscale-only as well? In that case, only the RGB-SSIM results would be valid...
And actually, thinking about it even more, converting to greyscale at the tail end just for Y-SSIM and IW-SSIM is fundamentally flawed (if it doesn't result in exactly the same bits as the luma plane), as now you're measuring distortion from an image that the codec was never asked to encode!