You are kinda missing the point there. It isn't about the main quest, it's about a coherent whole. If they are just random little stories that are connected to nothing then what is their purpose? You can just sit and read a book while the loading screens are on and the experience would be the same regarding the story. Planescape Torment's companions weren't tied to the main plot, but they were tied to the protagonist in some way. They also saw a kindred spirit in their suffering in The Nameless One. They had a reason to follow him and they all helped him to regain his memory. In KotOR2's case Kreia was the story, but the other companions are the Lost Jedi who had ties to important factions within the story. Handmaiden - Atris, Mical - The Republic, Visas - Nihilus, Bao-Dur - Mass Shadow Generator etc. The companions in MotB weren't tied to the main plot, but it was only possible because of their intervention, like I mentioned you couldn't assault the Fugue Plane without Kaelyn's army, you couldn't get the best ending without Gann's help and the story wouldn't start without Safyia.
That is what it's meant by coherent whole, not only tied to the main plot. They need a purpose in the whole thing and not just be random disconnected vacuum bubbles who are there just to fill space and words. Side quests and side characters are just that - side vignettes that can be optionally skipped. Companions are major characters who are with you the whole/most of the game and need a reason to be there.
