Answering my own question is always fun, especially the answer is "no, you can't do it."
After many Google searches, I've encountered the following article:
http://docs.codehaus.org/display/MAVENUSER/Default+Plugin+Execution+IDs
There is no way to separate configurations for command line executions of different goals in the same plugin.
Currently, the main plugin configuration section can be used to define settings to be used when executing a plugin from the command line. Unfortunately, these settings are applied to all executions of the plugin.