Well, yes, the control radar will interrogate IFF. But once launched the average anti-aircraft missile is largely autonomous these days. You don't want to have to keep your ground radar unit active and transmitting course-correction signals to your missile while said missile is in flight towards aircraft that could be armed with anti-radar munitions. I believe the Viet Cong learned that one the hard way.
But as you say, the airspace around Washington is busy so you need to be sure of what you're shooting at to avoid missing and hitting an innocent 747 just taking off. Or your shiny and expensive F-15s that have arrived on-site to intercept what you're shooting at...
As for the UL chap's concerns, I thought it intriguing. I know that modelling involves a lot of fiddling with variables and model types to get an accurate simulation. The company I used to work for did a lot of structural finite element analysis as well as computational fluid dynamics (not least for modelling fire and smoke propogation in one of the proposed replacements for WTC. I understand we did bid for the WTC collapse structural analysis but the Americans insisted the job went to a US entity). We burned a lot of CPU time.
On the one hand, the UL chap could be talking out of his hat about something trivial he only had a tangential contact with and/or was outside his area of expertise so he didn't understand what they were doing. On the other, he might be a serious FEA geek and really did see something dodgy going on in NIST's analysis and/or corners being cut. There's not enough evidence either way.
Nevertheless, I don't regard that claim on its own as evidence that the towers didn't collapse the way NIST says they did. More likely it's just sloppy modelling done under serious time pressure, as always. Compared to the rest of the supposition, wild claims and flat-out bullshit in "Zero" that was the only claim I hadn't heard before.