I don't use the collaboration messages, so I can't help you directly. But if you want to know where the ini file is used, then use grep to find all occurences of "collaboration.ini" in the PHP source code and inside templates.
You can post the enhancement requests in the bug tracker and optionally add them too the feature request list for eZ 3.9 ( http://ez.no/community/developer/specs/feature_request_list_for_ez_publish_3_9 ).
