The Organizational Chart for Jira comes in two types of modules. after installation, one primary chart would get installed on Jira Admin Page and for each project that is available, one project-based chart would get installed on each project.
Each chart has its own database and it is completely isolated from another charts. Of course, the primary chart would only be accessible by Jira Admins.
With this approach, you could visualize your employees and teams on the primary chart, and each team based of the project needs, could draw different chart to help them visuals their relation and members.
Some of other topics: