Could the original H. naledi "burial chamber" have originally been at a shallower depth?
2.5 million years is more than enough time for things to change drastically some places, in New Zealand there are mountains whose sediments were seafloor ooze a million years ago, but Africa is not usually one of them. Africa's geology is normally far too stable to show major changes on that short a timescale. In the normal course of things a given position in a cave system becomes shallower as time goes on due to surface erosion. What I can find on the Monte Christo Formation that holds the Rising Star Cave and the surface survey here suggests that there have been no major deposition events since the caves were formed, this would suggest that in fact the fossils were even deeper under ground when they were deposited.

It is however possible that there was a transient hole in the roof of the cave that has since filled with redeposited minerals and is no longer evident, such are not unheard of in karst terrain and would have supplied light to great depths. The bones may also have originated closer to the cave entrance and been swept deeper into the system by flooding at a later date.