I don't think MS will ever be customization-focused. They know people like to change the UI to their favorite color or whatever, and apply different wallpaper. Beyond that, I highly doubt they really care.
I also don't think they purposefully "hard code" anything in some kind of grand scheme to thwart customization. It's more likely to be an issue of laziness or efficiency on the part of their UI designers. Grouping multiple objects together so that they can be easily changed as needed with a single setting tucked away in some deep recess of the registry is likely easier to deal with that doing things separately. Especially when the needs of we few customization junkies probably doesn't even factor into the equation at all.
Also, I think some of it isn't even on MS's end, but Stardock's. I mean, SKS STILL has a lot of mislabeled settings and such, does it not?
Not to mention, a lot of things that apparently can't be changed or edited by WB CAN be changed with visual styles...