Oh of course you can also run it dry while running an OS, that does not matter much. I just mentioned it to avoid data loss from the to be happening sudden power loss. You really want to run it until the battery shuts off the system in hardware and not the OS deciding that it’s time to shut down because the battery is low - we do not want low, we want 0%. If your comfortable doing this while running your OS, sure, that’s fine too.
The charging after that in powered-off mode is just to avoid power budget interference with the charging, charging should then take place form 0% to 100% in one sitting and with the full charge current (which could get reduced otherwise if e.g. an OS is running).
Cheers
nicole