Yes authors of the paper cited in conformational entropy article assumed that backbone and sidechain entropies are uncoupled That was a valid approximation in their case since the backbone was fixed But the equation in  conformational entropy article is simply a general definition of entropy not necessarily conformational Note that pi can be a probaility of any state of any system I am not familiar with any publications that would say this equation is problematic The problematic can be only definition of states which is often indeed the case