From what I can see, most scalability settings that are saved get automatically reapplied next time the application is ran.
An exception to this appears to be foliage scaling. I managed to test this in a new project based on the FPS blueprint project. On each key 1…4 I set the foliage scalability setting (0…3 respectively) on the game user settings object and then called Apply Settings (which should save out the value and indeed does in my main project). I fill the floor of the map with foliage cubes and package a development build (shipping has the same problem of course, and Debug surely too).
Every time I restart the application, it does indeed recall the correct foliage scalability setting, but it isn’t applied. By default I see all the foliage until I press one of the keys and make sure the setting is applied.