Verstappen took pole at Suzuka by roughly six tenths ahead of McLaren duo Oscar Piastri and Lando Norris.
Having both drivers in the top three was a huge result for McLaren, but at the same time Stella felt it was humbling to see how much faster Verstappen was on the challenging layout, having hoped that his drivers would be closer to the Red Bulls.
"We expected to be more competitive than Singapore," Stella said. "We were unsure as to whether this would have put us as second best team, or whether Mercedes and Ferrari would have been there with us.
"We were pretty certain that Red Bull would have been the quickest car here, considering the track layout.
"If you look at the overlays, Verstappen gains in every kind of speed range, so it's quite remarkable. It gives us again the measure about how much work we have ahead of us."
He added: "In fairness, I would have expected to be a little closer. We are P2, P3, it's a good result for the team, but six tenths is a significant amount of work that we still have to do.
"In a way it puts us with the feet back on the ground, not that we have ever taken off at all, but quantitatively there's a lot of aerodynamic performance that we need to add on the car still."
While McLaren's top speed hasn't appeared as poor in Japan as previously in 2023, its weakness in low-speed corners remains an obvious handicap through Suzuka's tight hairpin and chicane.
"Both corners are poor. And we see in the GPS overlays we lose time compared to compared to many direct competitors," Stella acknowledged.
"We lose time through the mechanisms that we know we have to improve, so there was no positive surprise."
McLaren will therefore be looking over its shoulder at holding off the Ferraris and Red Bull's second car of Sergio Perez, rather than mounting a realistic challenge to beat Verstappen to the victory.
But Stella doesn't discount Mercedes either despite its disappointing qualifying performance, with Lewis Hamilton and George Rusell over a second behind in seventh and eighth respectively.
"The only way we can attack Max is tactical, should we be able for some reason to be ahead at the end of lap one," he added.
"But if he takes the lead, he just has so much pace that this is not going to be our race, or we are not going to be in his race.
"We are definitely in competition with Ferrari and Mercedes. Mercedes is better than us in terms of [tyre] degradation, so even if today they weren't as good as I was expecting they could be definitely in the game tomorrow."
