it's kind of handicapped to not put all planes on pentagon or something though
I mean what is killing civilians gonna do
Well, it pissed off a country enough to send them to war.
Flying planes into a large skyscraper is a very effective way of getting yourself/your message in the spotlight, and that's what it was really about.
Did the planes spawn in the city?
Not then, no, but there are airports around many cities.
Maybe I'm just overthinking on how to Self Delete bomb a country, but I'd take planes from airports relatively nearby.