That's how that value is stored. You are suggesting that, instead of a single place, it should be stored in two places. And I will have to deal with two ways to change it instead of just one. A player clicking the button is not a time-critical portion of code to facilitate this extra complexity.
It is also normal and intended for mods to change their own settings. Many indeed do so. The event being raised for all mods is also the intended modding API behavior. If some mod assumes it will only get that event for its own settings, that's a bug in that mod.
Looking at the Fill4Me code, it does indeed not differentiate between its own and other mods' settings getting changed. It's a bug in Fill4Me.