Verification done with bionic and cosmic; using the following config:

network:
    version: 2
    ethernets:
        ens4:
            match:
                macaddress: 52:54:00:ea:e6:7a
            mtu: 9000
        ens7:
            match:
                macaddress: 52:54:00:d7:62:4c
            mtu: 9000
    bonds:
        bond0:
            interfaces:
            - ens4
            - ens7
            mtu: 9000
            addresses:
            - 10.3.16.3/20
            gateway4: 10.3.16.1
    vlans:
        bond0.804:
            link: bond0
            id: 804
            addresses:
            - 10.99.99.24/24
            mtu: 1500
        bond0.8:
            link: bond0
            id: 8
            addresses:
            - 10.8.99.24/24
            mtu: 1500


ubuntu@apt-snail:~$ dpkg -l netplan.io | grep ii
ii  netplan.io     0.96-0ubuntu0.18.04.2 amd64        YAML network 
configuration abstraction for various backends
ubuntu@apt-snail:~$ ip link
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN mode 
DEFAULT group default qlen 1000
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2: ens4: <BROADCAST,MULTICAST,SLAVE,UP,LOWER_UP> mtu 9000 qdisc fq_codel master 
bond0 state UP mode DEFAULT group default qlen 1000
    link/ether 36:72:e5:93:2d:bb brd ff:ff:ff:ff:ff:ff
3: ens7: <BROADCAST,MULTICAST,SLAVE,UP,LOWER_UP> mtu 9000 qdisc fq_codel master 
bond0 state UP mode DEFAULT group default qlen 1000
    link/ether 36:72:e5:93:2d:bb brd ff:ff:ff:ff:ff:ff
4: bond0: <BROADCAST,MULTICAST,MASTER,UP,LOWER_UP> mtu 9000 qdisc noqueue state 
UP mode DEFAULT group default qlen 1000
    link/ether 36:72:e5:93:2d:bb brd ff:ff:ff:ff:ff:ff
5: bond0.804@bond0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue 
state UP mode DEFAULT group default qlen 1000
    link/ether 36:72:e5:93:2d:bb brd ff:ff:ff:ff:ff:ff
6: bond0.8@bond0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue 
state UP mode DEFAULT group default qlen 1000
    link/ether 36:72:e5:93:2d:bb brd ff:ff:ff:ff:ff:ff


ubuntu@humble-cattle:~$ dpkg -l netplan.io | grep ii
ii  netplan.io     0.96-0ubuntu0.18.10.2 amd64        YAML network 
configuration abstraction for various backends
ubuntu@humble-cattle:~$ ip link
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN mode 
DEFAULT group default qlen 1000
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
2: ens4: <BROADCAST,MULTICAST,SLAVE,UP,LOWER_UP> mtu 9000 qdisc fq_codel master 
bond0 state UP mode DEFAULT group default qlen 1000
    link/ether 62:61:81:9d:a9:6d brd ff:ff:ff:ff:ff:ff
3: ens7: <BROADCAST,MULTICAST,SLAVE,UP,LOWER_UP> mtu 9000 qdisc fq_codel master 
bond0 state UP mode DEFAULT group default qlen 1000
    link/ether 62:61:81:9d:a9:6d brd ff:ff:ff:ff:ff:ff
4: bond0: <BROADCAST,MULTICAST,MASTER,UP,LOWER_UP> mtu 9000 qdisc noqueue state 
UP mode DEFAULT group default qlen 1000
    link/ether 62:61:81:9d:a9:6d brd ff:ff:ff:ff:ff:ff
5: bond0.8@bond0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue 
state UP mode DEFAULT group default qlen 1000
    link/ether 62:61:81:9d:a9:6d brd ff:ff:ff:ff:ff:ff
6: bond0.804@bond0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue 
state UP mode DEFAULT group default qlen 1000
    link/ether 62:61:81:9d:a9:6d brd ff:ff:ff:ff:ff:ff

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https://bugs.launchpad.net/bugs/1804861

Title:
  MTU size defined on /etc/netplan/50-cloud-init.yaml not applied

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