Why Fake the Flight 93 Crash Site?

Because they didn't want any incriminating evidence at the crash site. The plane that witnesses around Shanksville saw flying crazily was probably a drone without passengers. If they crashed that, then they would have obvious plane debris and no dead bodies. This is particularly a problem in the rural area where the plane crashed, because local people might get to the site first and take pictures of plane parts that didn't match UA93. They would also wonder why there were no bodies around.

BUT-- if they create a crash site where it looks like the plane both disintegrated and disappeared into the ground, people aren't going to wonder too much about the lack of passengers because the plane is gone too. In the awfulness of the moment, people will simply accept the official story that the plane both disintegrated and disappeared into the ground.