I've tried to create a configuration file inside a folder, from the docs you say:
It is allowed to use relative paths here; just remember that these are relative from the working directory where you execute phpDocumentor in.
but it seems that the relatives paths are related to the configuration file folder, not where you run phpdoc.
In fact using ../../ etc to make paths relative to the config file it works fine
That appears to be an error in the documentation; this used to be true but was changed as the current behaviour is more logical and consistent with other tools (such as phpunit)
The documentation has been updated to reflect the new situation (http://www.phpdoc.org/docs/latest/for-users/configuration.html).
Thank you for reporting this error