I'm not to sure of what your asking. But here i will try an answers. I have been GM for about 10 years now. I like my player to have total freedom. Ok sometime i will have to agree that it's lead to stagnation or what would gamer call lag. But mostly all my players are totally free to do what they please. Just like any real man could. Of course i suggest them things, and when i want them to go somewhere and do my quest i find a way to appeal there character or force them by obligation. What i mean by force them isn't ''you go do this quest because i want it'' it is more like, what ever the character is in front of me he is a ''human'' with feeling, sense of duty/greed/power/love/etc. Well one way or another i get to know my player and character to a point then throw them quest so that they will do it.
As i recall they were walking on the road and they see a slave girl on the road. (quest suggested in gaia) I hardly though about the quest but still when with what the book suggested as it is a event in the story line. The character with high gnosis just happen to be there the good time good moment, just like written, my players in this game are so deeply good and honorable, they just sighed when they saw the girl and followed her without question i mean, i could have made an arch deamon or something, no real question ask, just do it because there honnor was commanding it. The same group of player in a game more evil would probably either had killed the girl, or rape/sell/take over the slave bussiness /ignore/ help her if in a good mood
Finally yes i do keep a main story and chapter as you say it, but take it as it is, if you are a bit gamer, i consider my game to be very bioware like. There is the main quest, and so many side quest. How you happen to evolve in the main quest, be a badass, a good guy, take romance, be a greedy bastard or so on is only up to you, if you like side questing and killing mobs too. If you like gambling or be a merchant would also be up to them. Of course, if they take to much time to do the main quest event happens, as the world just doesn't wait for them.