The Dutchman had a comfortable lead when Kevin Magnussen crashed and the debris trail he left led race director Niels Wittich to call for a red flag with three laps to go.
Verstappen was thus left on pole for a potential two-lap sprint to the flag but with a strong risk of losing the lead given that he had got away badly at the two previous starts.
In the event, Verstappen did get to the first corner in front and another red flag made it academic as the final race result order was in effect frozen at that stage.
"It was always going to be hugely frustrating when you get a red flag and a restart with three laps to go," said Horner when asked by Motorsport.com about the tricky circumstances.
"When you're the leader, you can only lose from that point. You can understand the rationale between wanting to finish under racing conditions rather than cruising behind the safety car for three laps.
"They might have been able to clear the circuit and get it going, I don't know. Like all these things, there's always something to learn."
The subject of using late red flags to ensure a finish under racing conditions has come up regularly in team boss gatherings.
In the past, the consensus has been that teams prefer to avoid them, but Horner says he's open-minded.
"It's something that has been discussed," he said. "I think there's always been a preference to finish under racing conditions, so if by stopping the race enabled them to tidy up the circuit, so rather than cruise out the remaining laps under a safety car, it's the right thing to do.
"The problem is, when you're the lead car and you've been controlling a 10s lead all afternoon suddenly it's a massive variable that becomes a bit of a lottery."
After the last red flag, there was some confusion over the final restart order for the one-lap run to the flag behind the safety car.
One version potentially put Red Bull's Sergio Perez ahead of Lance Stroll in fourth had order the safety car two-line order just after the previous start been used.
"As it unfolded, it was a case of did they cross the safety car line, it was another Silverstone [2022], basically," said Horner.
"We had tremendous support from the operations room as well, they have all the data in a calm environment, so basically they crunch the numbers and obviously Jonathan [Wheatley] working with his team as well. It was clear the race wasn't going to restart."
Alpine boss Otmar Szafnauer admitted that the team had hoped for the result to be declared before the final one-lap run to the flag, which would have left both Pierre Gasly and Esteban Ocon in the points.
"We definitely pushed because I don't know where we were at safety car line two, we would have been up there," he said.
"Safety car line two was before turn one. So Pierre probably would have been in fourth or something. For sure we asked them to do that. But I think they made the right decision. Those are the rules. So you've got to follow the rules."
Szafnauer did not question the need for the red flag triggered by Magnussen's accident: "I don't know all the circumstances as to whether that should have been a red flag or not.
"But having talked to the sporting director he believes that there was metal debris on the track, and therefore you have to get it off.
"If a wheel breaks up and you have magnesium shards all over the track, you've got to get that off. If it's rubber, that's a different thing. Even then, you don't want a piece of rubber flying up and hitting somebody at speed."
