Visual Effects were simply not this good and fluid in 2001… And I have first hand knowledge in this because I worked in that industry in Southern CA at the time.
I will say however that it is much easier to remove things than to generate them new in existing media. And it is also not so much about the quality of the CGI, but matching the CGI to the quality of the existing media.
Along with your North tower (1st plane)
Here’s a South Tower (2nd plane) video
