If playing the Civil War, the exchange of axes between Ulfric and Balgruuf can only occur if the main quest is active.
You are not stopped at the gates of Whiterun unless dragon attacks (Alduin) have begun. Prior to that, no Dragons are "awake." Even if you find the Dragon Stone in Bleak Falls Barrow, there will be no dialogue options to give it to Farengar if Helgen has not been visited first. There, you will witness Alduin attacking and a found journal will direct you to a few options to continue the Quest. Whichever start you choose, the main quest does not begin until you go to Helgen. I'm sorry if this is all complicated, but I'm trying to be as specific as possible. Could it possibly have an option to get arrested into Helgen and the game resumes as normal? That would make the Thieve's Guild or Dark Brotherhood starts even more awesome.
Hell this mod is pretty awesome and insanely well designed. Will it remain unaffected by you as long as you haven't started the main quest yet? I know that this mod DOES let you start into one of the factions I mentioned, but my question is, how does it work from there? If I chose one of these, how do I resume the main quest? Do I still get to witness Alduin attack Helgen, and from there it plays like the Vanilla game would? Until that happens, do normal Dragons still occassionally appear and kill everything like they would in the vanilla game? Also, remember that the Brotherhood Sanctuary has one of the Word Walls in it. I know, I know, it's childish and stupid, but GODdammit, I've worked hard for my Education and even harder to be a self-reliant grown man, I earned the right to be dorky once in a while! So I guess, this mod is gonna make me feel less guilty, if I played a scenario in which I was born into the Theive's Guild, and then graduated to the Dark Brotherhood, but in time, grew resentful of such life, and when I discover I'm the Dragonborn, I saw it as a chance to redeem my cruel past. Whichever you pick, the rest of the game is still the same, right? You become Dragonborn, and save the world, right? Well, it always bugged me that such a celebrated hero would suddenly join The Dark Brotherhood or the Thieve's Guild. I never used this mod myself before, and I'm thinking about it, and here's why. If you played this mod and know it in and out, you could help me with one thing.