You should be able to cook up a script that does this using the
CALIBRE_CONFIG_DIR environment variable described here:
http://manual.calibre-ebook.com/customize.html
You would likely need to have your script automatically set that variable in the Info.plist files inside the calibre.app bundle and then start calibre. Or you can just set the environment variable and then use the command line calibre.app/Contents/MacOS/calibre to launch calibre, but that may have some other side-effects siec you wont be launching the bundle.