Question: Can the system partition be safely erased with Secure Eraser?
Answer: Yes. The system partition is hidden in the "Drive/partition deletion" menu because it cannot be deleted during operation. However, if you proceed as follows, you can still clean up your system safely:
Reset your system to the factory state: Go to "Start" > "Settings" > "Updates & Security" and click "Recovery". In the right column under the heading "Reset this PC", click "Get started" and in the next step select "Remove everything".
Once the PC is reset, delete the free space via the "Free space deletion" menu in Secure Eraser. In this way, your system is reset to the factory state and all data is safely overwritten.