I hate it when people do this as it sounds super condescending. Literally talking down to someone like you would a small child that needed to be taught a lesson.
I think starting a thought with “So,” is some unholy mix of pseudo-California valley talk (not that valley) and upper middle class liberal arts in-speak.
For people with a bit of social anxiety, it can serve as an easy and comfortable lead-in to share a thought when they can't think of a better way.
Your second paragraph is probably one of the reasons people do it but it’s also the reason it come off passive aggressive, which when disagreeing with someone sounds condescending.
I hadn't considered it in the context of disagreement; I think I can see how that could rub people the wrong way.