One idea: once users and groups are in Bamboo, make project notification just specify which groups and/or users to notify. Each user can then decide how she wishes to be notified.

For example, project Confluence could notify: confluence-developers, jonathon@atlassian.com Each user would have a preference about whether they should be notified via Jabber, email or both.

There are many other possible solutions. I think we need a balance between administrator-configured notification (a la JIRA) and user-configured notification (a la Confluence). There are benefits to both.