There is a column marked "default" on the Jira Administration->Applications->Application Access screen. What does checking these boxes do?
Are these groups that a newly created user will automatically be added to assuming "Set Defaults for New users to" has that Jira application (Software or Service Management) checked?
If the above is true, what would be the effect of checking one or more of these boxes if my users and groups (outside of a single local admin account) are completely managed by LDAP which are sync'd via a SAML plugin on each login.