MiKTeX 2.9.6930 has been released on January 6, 2019.
In order to avoid leftovers, MiKTeX Console learned to reset the personal MiKTeX configuration if MiKTeX was installed system-wide:
This allows users to remove their MiKTeX related installation files before a system administrator completely uninstalls MiKTeX.
Prior to MiKTeX 2.9.6930, personal TEXMF root directories were visible (e.g., in MiKTeX Console) when running in administrator mode. This behaviour has been changed: in MiKTeX 2.9.6930 and higher, personal TEXMF root directories are blinded out when running in administrator mode.
Check for updates operation is much faster now.