I've got no answer for you unfortunately, but I wanted to make sure you were aware of our mega-AMA on Precolumbian Civilizations of the Americas tomorrow. If one (or more) of our relevant experts doesn't stop by to answer this question today, hopefully you can come by tomorrow and ask in the AMA.

The use of the dead to legitimate current political power is something very common cross culturally. I think three examples can be used to illustrate what I mean: First, in Archaic Greece, as the scattered populations began to coalesce into hierarchically organized communities old burial sites went back into use. That is, around the massive Mycenaean tholos tomb mounds the archaic elites would bury their own dead. This was a way of establishing a link between the current elite and the legendary heroes of old, who were assumed to be buried in the tholoi. In Ireland as well this was a common practice during the Iron Age, as elites attempted to establish themselves as the legitimate heirs to monumental Bronze Age sites, often by burying themselves nearby or erecting their own monuments. A third example is from the modern day, most explicitly with the burial situations of Mao and Lenin in the PRC and USSR, respectively. Giving them permanent publicly visible burial sites is a way to establish control over the legacies of their founders. In fact, this is a tendency you can see everywhere when you look for it, from various tombs of unknown soldiers to the literal concretization of an English cultural narrative in the walls of Westminster Abbey.

Hopefully someone with more specific knowledge of the Inca case can give an answer specific to it (I only have a fairly cursory knowledge of the topic) I just wanted to emphasize that while it seems shocking, it is actually perfect normal, just done with an Andean twist.