We don’t.
With that being said, we only promote a connection if it doesn’t already exist in the target environment.
The key here is to keep the CUIDs of the connections in sync between the environments and to use the same connection in all environments.
This doesn’t fit your scenario of wanting to be able to point your universe to different data sources though.
We use have some functionality configured to allow the users to change connections themselves using ODBC connections. See my post in this topic ODBC or OLE DB for MS SQL databases? for some more information.