I am pretty sure they all do, but thats a good question!
I know for sure camera settings don't change. My belief is that all these are 'set' on S2, the app simply facilitates making the setting.
Lets look at home point. What if you set home point (via app) then next flight you are somewhere else (maybe no app, or maybe with app). Does S2 retain the home point setting from previous flight? It might seem that it shouldn't, but I bet it does. The purpose of home point is for if comms are lost...if comms are lost, what the app has for a setting won't matter, so it MUST be a setting in S2.
These things hafta be durable settings in S2...and thus, if you are setting a home point, I think it should be reset first thing, every flight. Thats how my Mav was for sure.
FWIW, I don't want a home point set for beacon follow-me flights.