Bonded interface losing link each time netplan apply is run

Using netplan for bonded interface has the very serious drawback of losing link on all physical interface (bringing down the bonded interface) each time netplan apply is run, even if not changes where done at all.

Practical example:
root@ubuntu:/etc/netplan# dmesg -c
root@ubuntu:/etc/netplan# cat 00-installer-config.yaml
# This is the network config written by 'subiquity'
network:
  ethernets:
    enp0s3:
      dhcp4: true
    enp0s8:
      optional: true
    enp0s9:
      optional: true
  bonds:
    bond0:
      interfaces: [enp0s8, enp0s9]
      addresses: [10.0.0.1/24]
  version: 2
root@ubuntu:/etc/netplan# netplan apply
root@ubuntu:/etc/netplan# sleep 5; dmesg -c
[ 5375.046274] e1000: enp0s9 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX
[ 5375.206357] e1000: enp0s8 NIC Link is Up 1000 Mbps Full Duplex, Flow Control: RX

This is due to how netplan generate and networkctl interact:
- netplan apply calls netplan generate
- netplan generate recreates (unchanged) files in /run/systemd/network
- networkctl is called to reload the configuration
- networkctl recognize file timestamps are different and reconfigures the physical devices under the virtual bond interface, losing all links for these interfaces.

The current behavior is completely unacceptable because one uses bonded interfaces (especially in active-passive config) to *gain* reliability at the physical link level, not for losing it.

Regards.