I prefer to avoid customizing apps. I want to be able to sit down at a fresh install (or someone else's) and not spend time learning their preferences.
When someone asks me for a checkbox so they can have my app work their way instead and everyone else can do theirs, the hair stands up on the back of my neck. The check boxes are hard to discover unless you put them front and center, in which case they remain there forever serving no purpose.
I would rather redesign the entire interface, either to find the right answer that works for everyone, or to learn what makes one class of users different from another. The check box is a mode, and nodes are to be avoided if I possibly can.
I realize that this puts me at odds with a whole class of users who want to make their box do their thing. It's your box and you should do what you want. And I really love style sheets for that. Rather than cobbling together my own set of possible preferences you should have something Turing complete. Go nuts with it.
I think most non-Linux users haven't made a fresh install in 5-10 years. Preferences files and apps get transferred when you buy a new computer or update your os.