Your view of what constitutes a tool is overly broad. An OS is not a tool. A hand plane is a tool. It’s sharp and does one thing. The stuff an OS does might enable tools, and it may contain many tools, but it is not itself a tool.
A computer is also a tool that does many things and the OS is arguably the important part of how a user wields that tool.
It does variations of the same thing.
A computer is more of a toolbox than a tool.