The current behavior of presets in MatterControl(MC) is to "stash" your user settings when applied and "un-stash" the user setting when you disable the preset. If this is not the behavior you are experiencing you may want to check your version, We are currently on 1.7.0
Note: Changing the value after a preset was set it will override the preset but not save to the preset. This override will remain as a user setting after the preset is disabled
Edit: The behavior you are currently experiencing sounds like what we originally had where the user setting was always used if it was set.