That's not some minor quibble. It's a major flaw in his theory. He can't explain it because there's no explanation that doesn't strain the credulity even in his schizoid brain. "Guys, all they had to do was hijack four 737s fully laden with passengers and then land those jets unexpectedly before a state of emergency was declared without anyone realizing that it was unusual and then offload the passengers and kill them all, then activate the futuristic remote-control drone override box that maintenance personnel installed in the cockpits months before without anyone noticing and then take the planes off without anyone noticing and then put them back on their original route where their transponders were turned back on but no one noticed and then the empty places were remotely flown into the buildings, and all the hundreds of people involved in keeping this quiet would've had to remain quiet about the biggest and most complicated and most unnecessary conspiracy ever for two decades.

INB4 his argument is updated on the fly to "yeah well maybe all those passengers actually were on the planes in the first place! You can't prove they weren't knocked out with sleeping gas!" and he pretends he never said otherwise.

I've seen these arguments since the days of Loose Change when some 16-year-old schizoid claimed a single frame of footage was able to prove the planes shot a laser beam out before they crashed into the towers, as otherwise they would've turned into Wiley-E-Coyote on the superstructure.