Often it is used to have your specialised configuration. E.g. you copy the default configuration to a "myproject" configuration and can modify that while still having the default for reference.
If you are working with branches you might want to have a separate configuration for a branch as well, perhaps only for different files in deploy/.
It only adds to the flexibility. Just don't start a configuration twice at the same machine at the same time.
I already created a specialized configuration "custom" from a copiing the "default" one, but then I started this specialized configuration and only this one. What I mentionned in my original post is th epossibility to start "default" AND "custom" at the same time. In this case, what happen exactly ? do these configuration share memory space, class loaders or whatever ?