Enterprise features need upgrades to their configuration and implementation to be compatible with multiple organizations. Each upgrade can be it's own issue with more details/discussion.

• Group sync only works for the default organization. Also sync org membership. Multi-Organization Group Sync compatibility upgrade #14202
• Role sync needs to be expanded to allow assigning organization scoped roles Multi-Organization Role Sync compatibility upgrade #14203
• SCIM assumes the default organization when inserting a new user Multi-Organization SCIM compatibility upgrade #14204
• Workspace quotas needs to be reviewed. Given they are group synced, the primary work is to ensure the quota buckets do not leak cross-organization Scope quotas to an organization #14349

As it stands these features have no concept of multiple organizations, and reference the singular "default" organization.