Settings (both Editor and User-defined) are stored in standard UObject classes. The "mutable default object" if those classes is what stores the specific settings.
To access the "mutable default object" of a class you can use the unreal_engine.get_mutable_default(class)
function.
The following example code shows how to change the Editor/Appearance settings:
import unreal_engine as ue
from unreal_engine.classes import EditorProjectAppearanceSettings
from unreal_engine.enums import EUnit
# access the editor appearance settings
appearance_settings = ue.get_mutable_default(EditorProjectAppearanceSettings)
# print properties
ue.log(appearance_settings.properties())
# assign meters as the default distance/length unit (as list of values)
appearance_settings.DistanceUnits = [EUnit.Meters]
appearance_settings.save_config()
Another example changing action mappings of the input system:
import unreal_engine as ue
from unreal_engine.classes import InputSettings
from unreal_engine.structs import InputActionKeyMapping, Key
inp = ue.get_mutable_default(InputSettings)
km = InputActionKeyMapping()
km.ActionName = 'Kill'
key = Key()
key.KeyName = 'x'
km.Key = key
km.bAlt = True
km2 = InputActionKeyMapping()
km2.ActionName = 'Explode'
key = Key()
key.KeyName = 'y'
km2.Key = key
km2.bAlt = False
inp.ActionMappings = [km, km2]
inp.save_config()