That last one is talked about in the article -- it sucks!

I think if you were going to "downsample" for the purpose of creating a color set you could just scan through the picture and randomly select 10% (or whatever) of the pixels and apply k-means to that and not do any averaging which costs resources and makes your colors muddy.

Random sampling makes a lot of intuitive sense, but unfortunately doesn't work well. I just answered over at lobsters: https://lobste.rs/s/t43mh5/okmain_you_have_image_you_want_co...

I should probably add this nuance to the post itself.

Edit: added a footnote