The main idea behind FontBase is font activation/deactivation. The usual behavior, when you are using fonts without a font manager, is that they are basically copied into your system fonts folder and stay there forever, even if used once. After some time, you'll have a whole lot of fonts in your system fonts folder and this will lead to overall system performance drops and long app loading times.
Instead with FontBase, you can simply add fonts to it and activate/deactivate them when you really need to use them in your design projects or apps. They stay deactivated all the time and are not using any of your system's resources. You can also use the FontBase Auto-activation feature, to make your work with design documents much easier.