Hi Tim,
It would not be difficult to add a config setting that could make a global option for not showing module titles by default (it would apply to all sites in the installation would be the only drawback to the simple way to add this). I've made a note of it and wil try to get that into the next version.
Other feature specific setting defaults can be edited under Admin > Advanced tols > Feature Installation > Feature Settings, but they will be restored to what the developer configures them as in the feature config files any time you visit the /Setup/Default.aspx page.
Best,
Joe