I have read a few theories on this but the controlled demolition ones persist.
One of the problems is that some of the other theories also imply issues some people would not want to see the light of day. The article includes the issue of the role of fire retardent materials plays. The BBC did a film about this showing footage from the World Trade structures showing that the fire retardent material was insufficient even missing in places and reports had been written about this.
With high heats, and a lack of protection, steel conducts heat faster than the other building materials so the points of failure could be below the rest of the collapse. As well the structure will give before the rest of the cladding so puffs of material coming out below the collapse is not as strange is one might think.
In any case I am not buying the conspiracy theory as expressed but I do think the buildings had defects in maintenance -- maybe even construction -- which might explain why there is a preference to let the more outlandish conspiracy theories persist. If you have theories that persist that are outlandish there is less chance that the truth will be discovered and less credibility to the idea of something being hidden.
So there is a possibility of a coverup that is less wild than the one being promoted but still with an incentive to hide it and missdirect.