The Settings plugin currently provides a single very important function: Menu order!
Sure, it also displays the settings fetched from the initialization file, but that's not as useful as you can't change it.
Most of those values make no sense to change by the time the software have started, unless you are looking to restart it. The ability to shut down or restart the software from within the website is intentionally left out as they pose stability and security risk, so what good would it be to change the startup-settings?
No, better to gather other settings under the Settings plugin. For now, only a single function has presented itself to the need of such settings: The menu!
Each plugin registers zero or more menu items in a specific order maintained by that plugin. The order of what plugin gets it's entries listed in the menu used to be alphabetized. That was a deeply horrible idea.
We are accustomed to the Welcome/Landing/Home being on the left end of the menu, for example, and W is very far from the first letter of the alphabet.
It seems like a small thing, but being able to easily move the entries around is quite handy.