Do you have a source for who has asked the right question? You seem to know already, so what's the problem? Do you want it published in the NY Times or would some other publication be more satisfactory?
See John King's CNN report in the Anderson Cooper video linked above.
Rather than leave it as conspiracy fodder, the Air Force could have simply issued a press release saying "Yes, that was an Air Force plane" without going into any real details of what it was doing.
ETA: This aircraft probably rated a footnote in the 9/11 Commission Report.
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