By default, Atlas allows to link one Epic upon creation of a project. The real power of linking an Atlas project to a Jira issue would be realised if it is allowed to link it to something higher in hierarchy, i.e.: an issue type "project" or "initiative" that is the parent of a collection of Epics and forms an old-school project.
Otherwise Atlassian is just adding more confusion by now making projects (as managed in Atlas) equivalent to Epics. The risk of it is that reporting on a project will become an exercise of micromanaging which specific tasks have been completed since the previous report.
