When powering off (not rebooting) the Librem 5 battery should be put into shipmode in order to preserve its' capacity. For the whole discussion, see https://source.puri.sm/Librem5/linux-next/-/issues/120
When USB power is plugged in during powering off, we don't change any behaviour though. Setting shipmode in that situation would make charging stop when powering off. Of course this means that if the phone is shut down while plugged in and unplugged later, the battery will still discharge slowly.
Only when unplugged, running on battery only, during shutdown, we set shipmode and prevent the battery to discharge while the phone is powered off.