the options.txt isn't overwritten on update. So all the options should stay the same.
Would still be useful though. Lots of mods write to options.txt. Having a backup copy would let someone undo those changes if needed.
As for the rest of the options. It is annoying having to re set them every time. Not for sure how they would go about causing that not to happen though. Not for sure if they are stored with the configuration files or not.