Came across this today - https://learn.microsoft.com/en-us/sql/relational-databases/databases/rebuild-system-databases?view=sql-server-ver16#CreateMSDB

Gave it a shot on my cloned system & does get the MSDB setup as the correct collation. Still getting that same ConfigureSQLAlias...

Ok cool, thats pretty much what I was expecting the answer to be.

"Logins, Linked Servers, Audits, Jobs etc, anything that is in any folder in SSMS except the databases folder."

Is...