What led to the collapse is explained in pretty good detail. What the NIST is saying is that once the buildings themselves started collapsing, that's when they stopped the analysis of what was happening to the actual structure of the building. Because at that point, it's collapsing.

The physics behind why and how the buildings were brought to a condition where collapse was inevitable are well-known and well-explained. The physics behind what was happening to the structure of the building as it was collapsing are not well-known, and are very difficult to be well-known or explained because of the chaos and entropy that is occurring while a gigantic building is collapsing.

I believe you're misinterpreting this:

NIST’s reply denies the requests for corrections. However, it also mentions, “[W]e are unable to provide a full explanation of the total collapse” of the World Trade Center. In its final report on the Twin Towers collapses, released in October 2005, NIST admitted that its investigation did “not actually include the structural behavior of the tower after the conditions for collapse initiation were reached and collapse became inevitable”