I'm no expert on this, but I believe the Unraid Wireguard settings translate to a `docker network create wg0 ...` somewhere. When a custom docker network is created I believe the MTU option must be passed as an option, like: `docker network create wg0 ... -o com.docker.network.driver.mtu=1420` (or whatever you have set in the Wireguard settings page)
I'm guessing the existing MTU field currently only sets the `--mtu` option, and this only affects the default bridge network - not custom networks.
This can be verified by checking what options the bridge gets, by running this command: `docker network inspect bridge`. This has `com.docker.network.driver.mtu` to the value you input in the Unraid settings.
Now compare with the custom network (`wg0` in my case), which doesn't have any options at all: `docker network inspect wg0`
I have not found a way to modify the MTU value after the network has been created, so I think the only work around right now is to adjust MTU from within the containers. This is not ideal since the `ifconfig` command (or similar) must exist in the container, and it must also run as privileged.