Thanks for the report and sorry for the confusion regarding the different configurations. We'll fix that!
Mhh...
do you have the SaveConfig = true in your /etc/wireguard/wg0.conf?
From the wg documentation
SaveConfig — if set to `true', the configuration is saved from the current state of the interface upon shutdown. Any changes made to the configuration file before the interface is removed will therefore be overwritten.
I'm thinking if you had it in there, the wireguard interface is up with this configuration, you'll manually add a peer and then restart the service it would override your changes.