Avoid duplicating non-configuration settings when merging configurations

When one configuration inherits from another, we should merge the
configurations before merging the default settings into the configuration.
Otherwise, the more concrete configuration will end up with all default
settings twice

BUG=none
R=mark@chromium.org, thakis@chromium.org

Review URL: https://codereview.chromium.org/227693002

git-svn-id: http://gyp.googlecode.com/svn/trunk@1891 78cadc50-ecff-11dd-a971-7dbc132099af