Their 'problem' is they didn't want to make those extra keys in other color.
Odd that they make it fine in dark gray and in blue. Oh well, doesn't bother me personally, given the asymmetry with `~ and \| already. Plus stepped Caps Lock is best Caps Lock
It took me a while to realize what you've meant by this, but it makes sense now: their molds have more than one key, so they're putting in all of the same color plastic in that multiple-key mold, and the fulltouch caps lock key is part of a mold that has keys of all the opposite tone. So if they did a beige fulltouch, that means you also get these weird beige versions of other keys as well (like numpad 0, etc.), so that'd increase the cost of the sets because that's more plastic coming through. Still kind of sucks..
I'm guessing that the blue/gray sets are correct because they make full single-tone sets in each of those colors and just mix and match the mods. I don't think they make beige-only toned sets (they wouldn't be purposing them as inverted beige/white two-tone sets.. though that would be interesting).