It sounds like you found a bug. However, the man page for systemd-fstab-generator states the following (emphasis added).
systemd-fstab-generator is a generator that translates /etc/fstab (see fstab(5) for details) into native systemd units early at boot and when configuration of the system manager is reloaded. This will instantiate mount and swap units as necessary.
I think you can trigger a reload of the system manager by running systemctl daemon-reload. Do the automounts start working again if you run that command?