The Best Evidence
The official story about Atta’s Portland trip contains three mysteries:
Why were Atta’s bags not loaded onto AA 11? In the affidavit, pointed out a Newsday story in 2006, “there was no explanation of why they had not been loaded.” 
The loading failure could not be attributed to a late flight: The commuter flight back to Boston was on time, so there was an hour until AA 11 was to depart. 
This failure also could not be explained in terms of a careless ground crew, because “Atta was the only passenger among the 81 aboard American Flight 11 whose luggage didn’t make the flight, American sources confirm[ed].” 
Why would Atta have put his will in a bag that was to be loaded onto a flight he intended to crash into the World Trade Center?
Why would Atta have taken the risky trip to Portland?
The reasons why these three mysteries exist become understandable in light of news reports in the first days after 9/11:
According to CNN reports of September 12 and the morning of the 13th, two al-Qaeda operatives, Adnan Bukhari and Ameer Bukhari, drove a rented Nissan to Portland, stayed overnight, and then flew back to Boston the next morning in time to board AA 11. 
Materials that incriminated al-Qaeda were found by authorities in a Mitsubishi sedan, which had been rented by Mohamed Atta and then left in the parking lot of Boston’s Logan Airport. 
Up to that point, this had been the official story, but later in the afternoon of September 13, CNN apologetically reported that neither of the Bukharis could have died on 9/11: Adnan Bukhari was still alive and Ameer Bukhari had died the previous year. 
On September 14, although CNN continued to state that Mohamed Atta had left a rented Mitsubishi at Boston’s Logan Airport,  the Associated Press stated that the rented Nissan had been driven to Portland by Mohamed Atta, who with his companion “spent the night at the Comfort Inn in South Portland before boarding the plane the next morning.” 
This story still said that authorities had found the incriminating materials left by Atta in a rental car at Boston’s Logan Airport, although this part of the story was incoherent, because the new story entailed that Atta must have left his rented Nissan at the Portland Jetport.
On September 16, a full transition to what would become the official story appeared in the Washington Post: Besides stating that “Atta and Alomari rented a car in Boston, drove to Portland, Maine, and took a room Monday night at the Comfort Inn,” it also said that Atta’s incriminating materials were “left in his luggage at Boston’s Logan Airport.” 
By October 5, the FBI had created a chronology of the claimed movements of Atta and al-Omari in Portland on September 10, complete with videos and photographs.  Internal evidence, however, shows this chronology to be a fabrication. 
Internal evidence also shows that the aforementioned affidavit – which indicated that the FBI had from the outset claimed that (a) Atta had driven the Nissan to Portland and (b) the incriminating materials were found in his luggage inside Boston’s Logan Airport – could not have been written and dated on September 12. 
Summary and Conclusion
As shown by the evolution of the story about two al-Qaeda operatives flying from Portland to Boston, this story originally had no inexplicable mysteries.
But after it was realized that the Bukhari brothers could not have died on AA 11, the three mysteries –
why Mohamed Atta’s luggage was not loaded onto AA Flight 11,
why he put his will in a bag that was supposed to be loaded onto that doomed flight, and
why he would have taken the risky trip to Portland
– came about as by-products in the course of creating, over the course of several days, a revised version of the original story (according to which Atta and al-Omari replaced the Bukhari brothers as the al-Qaeda operatives who drove a rented Nissan to Portland).
Although this story is complex, it suggests that what became the official story was most likely based on creative imagination, not fact.