I usually oversimplify: "root" is a keyword typically used to be all incompacing. The system root contains all files in the system. The user root is a super-admin that has all user rights in the system. The group root is a super-admin group the root user is assigned to and has all group rights.
Note that, strictly speaking, this is a misconception. The root file system is the one which is at the root of the hierarchy of mounted file systems.
Even the notion of something being (or not being) "in the system" can be misleading, because today's systems, including storage devices, can be distributed in various ways.
The first program was also traditionally executed under a root user. You can see this carry forward with init scripts running as root by default.
There are no root "permissions", because permissions are not a tree structure. Users can't give permissions to other users, recursively.
If each capability (cross the namespace or object to which it is applied, for non-global capabilities) is a leaf, then the global capability itself is a branch from which all of those leaves have sprouted, and the set of all capabilities live in a tree...
There is Root at the base of the trunk uniting all of the branches.