I think what they mean is, having all the source code that make up your system as well as building everything yourself, allows you to climb down to any level of the system and adjust the parts as needed, including the compilers and build system. It gives you full control of everything running on the machine.

This kind of control is not commonly seen because most people don't want or need to build it all from source. But it makes sense in some contexts, like for embedded or security critical systems.