At the moment there is some duplication of the properties (for historical reasons, bootstrap was developed after the initial integration). So, e.g. Galaxy credentials are specified one way for GalaxyConfigurationBuilder:
http://www.mulesource.org/display/GALAXY/Mule+1
, but differently for Mule Bootstrap: -M-Dgalaxy.username
These should be unified for consistency. E.g. using ad-hoc System properties could be the way to go, as it doesn't require hacking any startup script and is already used throughout the startup process in several places. Additionally, defaults can be used for credentials to simplify initial setup.