Define "user configuration"? I would recommend leaving the ACAD.CUIx file alone. Possibly the full treatment of placing it in a common network location and make it partial to a custom Enterprise CUIx. Use a per-user custom Main for storing the workspace.
Fastest (but not necessarily best) way of restoring everything is to delete a non-active profile and reload from an ARG file. That changes nearly everything but all at once (no pick and choose), and does nothing about the workspace unless the Main and/or Enterprise are changed.