The rules of the contest say:
"Photos submitted to Picture of The Year must be a truthful representation of whatever happened in front of the camera during exposure. You may post-process the images electronically in accordance with good practice. That is cropping, burning, dodging, converting to black and white as well as normal exposure and color correction, which preserves the image's original expression"
My personal belief is that the judges went too far in the interpretation of their own rules because I think main changes the photographer used between developing the raws (some have extreme ETTR for other IQ reasons) and the finished publication is levels, saturation and contrast. I agree the final pictures are quite contrasty and saturated, but I think this type of processing increases the impact of the message the photographer is giving about the environment he shot.
In my mind he did not alter the colors of his original capture (contrary to what one of the judges says), we all know that especially with level adjustments the saturation gets impacted. That's why the very pale yellow chair is now bright yellow, that's why an almost grey wall (with just a tad blue hue) is now bright blue. As far as I can see no colors were "replaced" by others, only relative luminosity and saturation changes. I wouldn't know how to do it, but I think with extreme developing techniques you could have produced color slides that looked close to his final images, and therefore the series should in my mind not be disqualified.
Just my $0,05, but remember when you submit pictures for a contest, the jury is always right. The only freedom we have is to disagree with them.