I found a temporary fix here. Go into Program Files\Unreal Engine\4.0\Engine\Config, back up your BaseScalability.ini to some other folder, then change every single value to the one you want.
For example, change [ResolutionQuality@3]
r.ScreenPercentage=-1 to [ResolutionQuality@3]
r.ScreenPercentage=50 etc.
Then when you package your game it’ll use these settings. Unfortunately this means every one of your end-users has to play the game using your settings.