How would that be in any way related? I mean they don't limit you to one or two teams so the story should play out no matter which team you choose because the parameters stay the same. The only reason I can think of would be voiced cutscenes in which players mention their team but even that would not make sense since you can actually do trades so you could move players around anyway... so... yeah it doesn't make any sense at all.
I asked people on a modding community to look into overriding the original roster with custom rosters for that one mode. Don't know if it will work but this just seems absolutely silly to me.