Only 'master' inside the system databases in Azure Managed instance During our POC we saw the system databases(model,msdb and tempdb) lying outside the system databases group.

Any specific reason behind it?
It was just because of the SSMS version. https://stackoverflow.com/questions/54695590/create-database-using-ssms-gui-fails-for-azure-sql-managed-instance  

Used 17.9.1 and can see things lined up properly. Probably the previous version was treating as Azure database.