We are having a recent Arch Linux here, but unfortunately the MTUBytes option seems to get ignored for GRE tunnels:
$ cat /etc/systemd/network/31-somename.netdev
Even after a complete system reboot the MTU is set to 1476 instead of 1400.
$ pacman -Qs "systemd"
systemd client libraries
system and service manager
local/systemd-sysvcompat 218-2 (base)
sysvinit compat for systemd
I am pretty sure this has long been fixed, the current code explicitly sets IFLA_MTU for all interfaces that are created. If this still is a problem, please open a new issue on the github instance.