I think I understand what you describe. However Geany, to my recollection is the _only_ application that yields that erratic behaviour — as far as I remember of my 20 years using Linux, of course.
How about saving the configuration when it _actually changes_ instead of on exit? From what I know a lot of Linux applications do this, be it on a timer to avoid frantically committing to the disk if the user does change a lot of parameters in a short time.
I'm sure the design is as it is because there are reasons (which I'm not aware of) but that design choice itself causes this issue to happen in this case, right?