I missed some relevant logs:

SCPlugin-Ifupdown: devices added (path: /sys/devices/virtual/net/eth0.1, iface: 
eth0.1)
SCPlugin-Ifupdown: device added (path: /sys/devices/virtual/net/eth0.1, iface: 
eth0.1): no ifupdown configuration found.

>From that, I think I found the root cause. After doing "apt-get source
network-manager" and grepping for "no ifupdown configuration found", I
looked in src/settings/plugins/ifupdown/plugin.c and found the function
udev_device_added(), which does a g_hash_table_lookup() to find out if
the interface is managed or not.

It appears that NetworkManager doesn't ever refresh its idea of the
interfaces list. So if you edit /etc/network/interfaces, NetworkManager
doesn't update its internal hashtable of unmanaged interfaces.

Therefore, the following is a workaround:

sudo invoke-rc.d network-manager restart
sudo ifup <desired-unmanaged-interface>

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https://bugs.launchpad.net/bugs/1439436

Title:
  NM in vivid tries to take over my libvirt bridge, deconfigures its
  address

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