When I get my wooden palette, I plan on painting it a mid-value neutral gray. It should be easier to judge value etc. that way. I love natural wood tones, but if they might throw off my ability to judge color/value, I am happy to paint over the natural grain.
As far as the box goes, wouldn't a plastic storage box of similar dimension, with a lid be good? I use the Masterson palette box now, which would be too small, but it doesn't seem to be a whole lot more than a plastic storage container when it comes right down to it.