My thoughts about that were so far: when the defaults are stored in the config file, and they will be changed in the future (e.g. replace 'Monospace' by 'Comic Sans'), then every user will find the same layout as before after an update. This can be good (no changes for him) or less good (he will not notice that some improvements were made). 
So, probably things like the font family or the tab width may not be stored, but the current flags indeed should *not* be stored. That's why I did not add an if to every single line.