I believe the official view does state that they were weakened - but they do not use the word "melt" as you are doing. That is a huge difference.

Burning fuel, not to mention other materials in the building, can create heat that would weaken the structure - but not "melt".

Your inference gives an impression that the steel melted away, and if you saw the site you would have realized that the beams did not disappear.

You also need to add the stress caused by the impact of the planes that damaged the core. It was not simply the fires.

The Madrid skyscraper is not a apt comparision because
a)the buildings were not the same construction.
b)the Madrid skyscraper was significantly smaller
c)the Madrid skyscraper did not suffer structurual damage from a plane loaded with fuel crashing into it at 500 miles per hour

You are right, thermite could also cause distress to the steel - but no one has shown any logical way that the thermite could have been planted in the building and orchestrated in such a fashion.   

It does not make any sense that a plot would have been approved that would require a Rube Goldberg plan that requires that many steps and points of complication. That is the crap of science fiction that depends on a reader dropping all logic to accept the premise.

Also, here is a Canadian report on the collapse - A Canadian Report