SystemTweaker only applies the tweaks that the user chooses to apply. This is usually done by ticking the checkboxes next to the titles of the tweaks that the user chooses. The tweaks can be enabled or disabled in this manner, however SystemTweaker also allows the user to easily revert all the changes that were made since it was installed.
When SystemTweaker is run for the first time, it takes a snapshot of the Windows settings as they are before any tweaks are applied by the user. The Restore Windows Defaults button at the bottom of the Tweaks tab restores the settings as they are in this snapshot so that any changes made by SystemTweaker can be easily reverted.