It's fine the first few times through the game, but like the cart and dragon attack part of Skyrim, it's kind of a waste of time when you just want to jump into the game.
I don't like the 111 crawl at all, since it's very obviously a training dungeon, and it's a big waste of time. I don't know if they're considering that at all. I don't speak for the team at all, but once all the story chapters are finished, alternative takes where Jake and others play along with you not being Shaun's parent might be possible. In fact, it's somewhat in favor of it as it focuses on you rebuilding the Commonwealth.
That being said, a lot of us do use alternate start mods and divorce ourselves from the role Bethesda set out for us, and Sim Settlements 2 as a project is not directly opposed to that. It can't possibly account for all the story mods that change the core story of Fallout 4. Sim Settlements 2's story is based on the Sole Survivor being the parent of Shaun.
