Stewart revealed that all of the characters in the Illuminati scene filmed their portions alone. Raimi then used clever special effects to make it look like they were all in the same room. Much of the Marvel Cinematic Universe is filmed in front of a green screen as it is, so compositing a group of actors into the same space wasn’t anything that necessarily stood out, visually. It did, however, alter the way the actors might have played the scene otherwise. Perhaps to leaven the one-actor-at-a-time restrictions of the scene, the Illuminati were all seated on thrones about eight feet apart and never had any moments when they interacted face-to-face.
Stewart seems to have encountered this kind of shoot a few times recently in his career, saying:
“I was alone. In the big scene, each one of the leading actors had the same experience; they were shot on their own. It was frustrating and disappointing, but that’s how it has been. The last few years have been challenging.”
Stewart has famously said that he’s always felt more at home on the stage than in front of cameras (although he seems to be pleased to work in either medium), so it’s reasonable that he prefers traditional interactions with his co-stars.
That said, Stewart also noted on the “Happy Sad Confused” podcast that he prefers solitude in some cases. He likes going on long walks by himself, allowing his mind to wander and explore whatever character or material he may be studying at that moment. This is also an actor, recall, who staged a famous one-man version of “A Christmas Carol.” It was the Professor X scenes in “Doctor Strange” specifically that bummed him out.