In my test I modified a multipass launched VM's netplan config to:

multipass@safe-hornet:~$ cat /etc/netplan/50-cloud-init.yaml 
# This file is generated from information provided by
# the datasource.  Changes to it will not persist across an instance.
# To disable cloud-init's network configuration capabilities, write a file
# /etc/cloud/cloud.cfg.d/99-disable-network-config.cfg with the following:
# network: {config: disabled}
network:
    ethernets:
        ens3:
            dhcp4: true
            mtu: 1496
            match:
                macaddress: 52:54:00:4c:5b:ac
            set-name: ens3
            dhcp4-overrides:
                    use-mtu: false
            dhcp6-overrides:
                    use-mtu: false
            ipv6-mtu: 1284
    version: 2


Also disabled cloud-init overwriting it:

multipass@safe-hornet:~$ cat 
/etc/cloud/cloud.cfg.d/99-disable-network-config.cfg 
network: {config: disabled}

IPv6 MTU is properly set on Eoan after reboot:

multipass@safe-hornet:~$ sysctl net.ipv6.conf.ens3.mtu
net.ipv6.conf.ens3.mtu = 1284

... but not on Disco or Bionic. To be continued...

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https://bugs.launchpad.net/bugs/1671951

Title:
  networkd should allow configuring IPV6 MTU

Status in cloud-init package in Ubuntu:
  Confirmed
Status in netplan.io package in Ubuntu:
  Fix Released
Status in systemd package in Ubuntu:
  Fix Released
Status in cloud-init source package in Bionic:
  Confirmed
Status in netplan.io source package in Bionic:
  Fix Released
Status in systemd source package in Bionic:
  Triaged
Status in cloud-init source package in Disco:
  New
Status in netplan.io source package in Disco:
  Fix Released
Status in systemd source package in Disco:
  Triaged

Bug description:
  = netplan.io =

  [Impact]

   * IPv6 traffic failing to send/receive due to incompatible/low MTU
  setting. Specifically, IPv6 traffic may have higher MTU requirements
  than IPv4 traffic and thus may need to be overridden and/or set to a
  higher value than IPv6 traffic.

  [Test Case]
   * Apply a netplan configuration that specifices ipv6-mtu:

  network:
    version: 2
    ethernets:
      eth0:
        dhcp4: true
        dhcp6: true
        ipv6-mtu: 6000

   * Check that MTU bytes, is at least IPv6MTUBytes on the interface:

  $ sysctl net.ipv6.conf.eth0.mtu
  net.ipv6.conf.eth0.mtu = 6000

  [Regression Potential]

   * This is a future compatible backport of an additional keyword not
  used by default. It may result in MTU change to a higher value, which
  should not cause loss of connectivity.

  [Other Info]

   * Original bug report below

  = end of netplan.io =

  = systemd =

  [Impact]

   * IPv6 traffic failing to send/receive due to incompatible/low MTU
  setting. Specifically, IPv6 traffic may have higher MTU requirements
  than IPv4 traffic and thus may need to be overridden and/or set to a
  higher value than IPv6 traffic.

  [Test Case]

   * Use IPv6MTUBytes= setting in a .network unit
   * Restart systemd-network
   * Check that there no error messages / warnings about not-recognizing this 
option
   * Check that MTU bytes, is at least IPv6MTUBytes on the interface

  [Regression Potential]

   * This is a future compatible backport of an additional keyword not
  used by default. It may result in MTU change to a higher value, which
  should not cause loss of connectivity.

  [Other Info]

   * Original bug report below

  = end of systemd =

  1) Zesty
  2) systemd-232-19
  3) I need to configure the IPV6 MTU for tunneling by adding an 
IPv6MTUBytes=1480 value in the .network file for an interface with an IPV6 
static address in the [Network] section
  4) networkd does not parse or read the value and does not apply this 
configuration to the interface.

  Upstream has discussed this issue here:

  https://github.com/systemd/systemd/pull/1533

  But it's been closed in favor of only setting via RA.

  However, we know of multiple use-case which are currently supported in
  ifdupdown where we want to retain control over IPV6 MTU values outside
  of PMTU Discovery configurations.

  Some context from those discussions

  >> Client systems that route their ipv6 packets to a 6in4 router also
  >> have to have their ipv6 mtu lowered.  They could lower their link mtu,
  >> so their ipv6 packets are small enough, but that reduces performance
  >> of their ipv4 network.

          Yes.  Anything that creates a PMTUD black hole can result in
  situations where the higher header overhead of IPv6 will cause IPv4 to
  pass but IPv6 traffic to be dropped.

          One example here is egress from an ipsec tunnel wherein the next
  hop MTU is too low for IPv6 datagrams to pass.  Another is VM ->
  whatever -> host bridge -> tunnel ingress.  If the datagram cannot enter
  the tunnel due to size, it is dropped, and an ICMP response uses the
  tunnel address as a source, which may not be routable back to the
  origin.  This one is an issue with IPv4 as well, and is one case where
  manually setting the IPv6 MTU lower than the (also manually set) device
  MTU is of benefit.

          In essence, any of these sort of cases that require an explicit
  setting of the device MTU will likely require a setting of the IPv6 mtu
  as well to account for its larger header overhead.

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