Possibly the frameset pricing is set higher because if there is a robust market in framesets it would cut into the sales of fully built bikes. As that would cut the number of components they have to purchase, they loose some of their discount for those components.
Also I wonder if those that purchase a frameset only might not be more troublesome and costly to the mfr because the buyer didn't fully understand what components will work with that frame and what won't. Or those that want to use a hammer to install their bb and other such stuff.