The SDE user is what we call the geodatabase administrator. They own the set of repository functions that allow the DB to perform the functions of a geodatabase. So yes, SDE is the Esri provided schema.
To be honest, you do not know if someone has changed the underlying tables. However, the ArcGIS client will update them as needed to register the items for use within the Esri and other ecosystems.
We used to have something like the 2 DB model, but they got way too complicated and created "double" the administration overhead.
You can have other users (i.e. GIS, DATA, DATAOWNER, etc.) own data in their specific schema. We highly recommend that you have a data owner that is not SDE.
Hope this helps!
--- George T.