I'm not sure I get what you think the structure should be. I do agree that
1. config is more appropriate for ... config
2. the module name appearing twice feels cumbersome. Maybe something like /modules/$type/$name/module.xml or even applicationContext.xml would do, especially if we finally zip that whole thing. You don't want to have to open up the zip if you rename the module, so having a well known xml file name makes sense I guess.