Saving to engine.cfg

func _ready():
    set_value("application/name","Some example name") # key MUST BE LOWERCASE, it's capitalized inside project settings!
    # After doing that, go back to project list and reopen your project
    # It modified your engine.cfg

func set_value(key, value):
    Globals.set(key,value)
    Globals.set_persisting(key,true) # unnecessary if you checked checkbox on to the left of the property in Project Settings
    # ^ non-persistent properties will be reset after reopening the app/project
    Globals.save() # save to engine.cfg