The idea of attacking the twin towers for whatever reason was floating around.

That’s true; there were several depictions of the WTC being attacked in popular culture and the media before and around this time. Examples range form Boots Riley’s album cover to cartoons (there was an incident in GI Joe or the Transformers IIRC).

What makes the Lone Gunmen instance stand out, to me, is a couple specific details that coincide with the real event and are unmatched by any other portrayal (that I’m aware of), namely, it:

• Involved a domestic civilian passenger airliner departing Boston Logan International Airport
• Was perpetrated by the US national security state in a false flag attack to advance its own interests

Show creator Chris Carter developed a working relationship with the FBI during the production of the X-Files, which makes it plausible that someone spilled the beans to him about actual goings on.