While we don't have an internal community, we do have our knowledge base housed in a private space. All of our support content is stored in this one space which should allow for easy searching. One issue that we've run into is when our support team is answering a question (housed in a less-private space) and trying to link to content in the knowledge base, some members are not able to view that content. This same issue could happen with you if a person is a member of multiple groups and tries to link content from one to the other.
If you have any questions on how we utilize this in an external community, please let me know and I'd be happy to help!