The main source of our information about al-Qaeda's planning of the attacks is the interrogation testimony that the captured members of the organization, primarily Khalid Sheikh Mohammed, gave the CIA (under infamously dubious circumstances of coercion), which are presented in a narrative form in the 9/11 Commission Report. It does not describe what they thought would happen to the towers after they were hit with the planes. The main relevant passages state that:

KSM [Khalid Sheikh Mohammed] acknowledges formally joining al Qaeda, in late 1998 or 1999, and states that soon afterward, Bin Ladin also made the decision to support his proposal to attack the United States using commercial airplanes as weapons. [...]

KSM has insisted to his interrogators that he always contemplated hijacking and crashing large commercial aircraft. Indeed, KSM describes a grandiose original plan: a total of ten aircraft to be hijacked, nine of which would crash into targets on both coasts-they included those eventually hit on September 11 plus CIA and FBI headquarters, nuclear power plants, and the tallest buildings in California and the state of Washington. KSM himself was to land the tenth plane at a U.S. airport and, after killing all adult male passengers on board and alerting the media, deliver a speech excoriating U.S. support for Israel, the Philippines, and repressive governments in the Arab world. Beyond KSM's rationalizations about targeting the U.S. economy, this vision gives a better glimpse of his true ambitions. This is theater, a spectacle of destruction with KSM as the self-cast star-the superterrorist. [...]

Bin Ladin reportedly discussed the planes operation with KSM and Atef in a series of meetings in the spring of 1999 at the al Matar complex near Kandahar. KSM's original concept of using one of the hijacked planes to make a media statement was scrapped, but Bin Ladin considered the basic idea feasible. Bin Ladin, Atef, and KSM developed an initial list of targets. These included the White House, the U.S. Capitol, the Pentagon, and the World Trade Center. According to KSM, Bin Ladin wanted to destroy the White House and the Pentagon, KSM wanted to strike the World Trade Center, and all of them wanted to hit the Capitol. No one else was involved in the initial selection of targets.

Which is to say, their way of talking about the aftermath plan — at least according to this source in retrospect — was more about the symbolism of it than any specifics about the engineering.

Given that to anticipate their collapse would require a detailed understanding of their internal structures and also anticipating exactly what would happen if a jet crashed in to them (the prolonged heating and burning, for example), it seems highly unlikely that he would have been able to predict this without doing extensive studies that it does not seem (at least from the 9/11 Report) that anybody ever contemplated doing, much less actually did. The collapse took the American first responders entirely by surprise, and likely took al-Qaeda by surprise as well.