Okay...
First off, since you are not hosting, your game configuration settings will not affect the execution of a turn. To say that they are meaningless is however not quite correct. For example, if you have FOW turned off in your configuration, when you load the .hst file your opponent has just sent you, you will immediately quit the game,
and possibly move to a new city on panic, when you see all of your opponent's units on the map

bad mojo
I can't think of anything else except maybe the Traffic Rule, which would show different movement times for your stacks than during the actual turn execution.
Having one installation per opponent you are playing is like having one car for each radio station somebody in your family listens to, because your radio doesn't have buttons and you have to dial in your station every time after your son has
borrowed the car and left his techno hyper trance *CHUNGA*CHunga*chUNGA*fweep*fwuuum-fwoop-fwoop* "
music" at volume 9000 playing on the radio

.
You actually only have to save a General.opt file for each opponent, and implement the correct one before starting the game and loading the .hst file.
and maybe one day Pocus will put buttons on the radio
