The sd9 was the first attempt at a completely new technology. Since that model, sigma/foveon have worked hard at taming colour issues as have the Bayer manufacturers.
None of them make cameras/software that yields forensically accurate colours - you can see this is tests, there is always some deviation from neutrality.
Usually that is deliberate: everyone is trying to find the magic formula that yields both believability and emotionally satisfying colour. It's not an easy balance to strike because they can't stray too far from neutrality because people have got used to digital colour being much more accurate than film and spot wrongness quickly.
Foveon has the most difficult task of all because the silicon depth filtration technique isn't very good at colour: it needs a lot of software tweakery. Gradually they are getting a handle on it and the Sd15 is pretty good (for a Foveon).
The SD9 is interesting. I regard its colour as a bit of an abomination but like any dramatic deviation from neutrality it provides opportunities for a different look if that is what suits a particular artistic requirement. Much like Cokin startburst and tobacco grads it has its place. For everyday regular straight photography, however, the permanent yellow cast, false polarised sky blue and feebly desaturated greens can be a challenge. I think of the SD9 as a special effects camera, useful when a certain look is desired but a liability for standard use.
As to why there has been a sudden re-newed appreciation of this prototype camera, I'm not sure. Maybe it's a reaction to the homogenisation of colour responses across brands that is the result of the improved colour accuracy offered by digital? In the film heyday you had a wide range of different colour interpretations available. If you wanted strong colour, you had Velvia and Kodachrome, for neutral colour you had Provia and Astia etc etc.
The thing that is maybe missing in the minds of a lot of digital photographers, is a realisation that digital colour is not a fixed look you have to buy into and can't change. Use the Adobe DNG editor and you can choose your own look by creating your own contrast curve and colour assignments. It's something that is rarely discussed or taught, but the option is there.
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