One of the more obscure permission-bits is called setuid, which may permit a program created by, say, root to execute with root's privileges rather than your own.
Nevertheless, not all installations manage everything using the root user. For example, in my tiny shop, all non-system applications are owned and installed by a non-root "maintenance user" (that's my term...) whose only purpose is to install programs ... and to own what has just been installed. This user doesn't have the privilege to install things in /usr/bin but instead installs them somewhere in /usr/local.
And so it goes. Programs which are "part of the Linux system" live one place, while programs which are system-wide user applications live elsewhere.