It seems that the configuration does not allow the use of the global passwords. It would be a nice way to keep secrets in configuration files. For instance, take a .pypirc file:

[distutils]
index-servers =
    PyPI

[PyPI]
repository: https://pypi.python.org/pypi
username: jenkins
password: ${PYPI_JENKINS_PASS}

It would be great if we could store PYPI_JENKINS_PASS in the global passwords and access it from these files, so that it would parse them at write time.