Generally the stuff in settings.json but not in-game settings is there because it would have to be done to a different level of quality for me to feel comfortable having it be an actual in-game setting.
In the case of ship explosions, for example, they "work" for frigates, but when you scale them up for larger ships, they could stand to have more detail if viewed stand-alone. With the whiteout over them, this never comes up - but removing whiteout would make this an issue.
If tweaked from a config file, though, I think there's an implicit understanding that things may or may not be optimal as a result of the changes.