Lando Norris had fought his way to the front in mixed conditions early in the race, working his way past eventual race winner Max Verstappen and polesitter George Russell.
But Norris and the team turned down the option to immediately respond to the first safety car of the race, after Logan Sargeant shunted his Williams at Turn 6, and instead toured slowly behind Bernd Maylander's Mercedes while his rivals opted to switch tyres.
By the time Norris stopped a lap later, he found himself back behind the Red Bull and Mercedes.
Asked whether there was any reason other than the timing of the first pitstop that contributed to Norris missing out on a second win of the season, Stella replied: "Not later in the race.
"I think later in the race, things unfolded... Mercedes should have finished ahead of Lando.
"So if anything, we maximised what was available after the safety car. Without the safety car, then I think Lando could have accumulated such a large advantage that then we could have tried to make it to the end on the dry tyres."
But suggesting even a large gap wouldn't have guaranteed victory as the track dried out, Stella added: "I think Mercedes, they could have caught up - because they were a few tenths of a second faster than us.
"We really needed a decent advantage to make it safely to the end. But obviously, this is a little bit academic because in a race like this [with] two or three safety cars... you have to assume they will happen and also, the weather was around.
"We knew that it was going to be a race decided by various scenarios and ultimately, I think we are happy with the results."
Norris had stretched out a sizeable gap over Verstappen and Russell in the first stint, with the McLaren coming alive around 15 laps in.
The Briton and team-mate Oscar Piastri began lapping over a second faster than the squad's rivals as the track dried and everyone remained on intermediates.
Strategy was complicated by the threat of further rain just before the midway point of the race and when explaining how his drivers extracted so much performance, Stella referred to the second weather front.
"We knew that it would not have been easy to make it to the rain expected around lap 30 initially, it would have been difficult for the intermediate tyres to survive that long," he explained.
"So because we had no pressure, we started to save the tyres very, very early, even when [it] kind of wasn't necessary, trying to find the cold patches or wet patches to make sure that the tyres stayed in good condition for when the track would have been more challenging.
"There's no magic, it's just the position we were in the first stint meant that we could apply this strategy with no loss - because we didn't have pressure from behind."
Watch: Canadian GP Race Review - Wet and Wild Vs Cool and Calm
