Let's see...
Yeah, agree that the glass pentaprism is probably a big factor. It might have a thicker gauge metal for the frame and of course (most of) the exterior is magnesium alloy instead of plastic.
The SR mechanism and AF are more advanced, so they might require more components and materials to do it. The circuit board and such probably has more RAM and other components compared to the K-r. Other stuff like the motor that drives the mirror flopping probably has to be bigger to handle the higher FPS.
It all adds up.