Note since this is a linear approach, the choice of the colorspace can have a large impact on the results. You didn't mention the colorspace, my best bet is that you used sRGB. Maybe you can try it on a linear colorspace too.

Edit: According to the source you use PIL.Image.getdata(), which according to the doc returns "pixel values", then they have an RGB->XYZ conversion example that only works for linear colorspace. So it suggests that they already return linear RGB values, but many software mess these things up so I'm not 100% sure.