I tried this variant to tell NetworkManager to ignore the virtual devices:

[keyfile]
unmanaged-devices=mac:xx:xx:xx:xx:xx:xx

(using the real MAC address of course)
It still does not change anything.

But I noticed this in the log, which happen whether or not the unmanaged-devices option is set:

Aug 19 18:52:04 n55sf-l NetworkManager[6399]: nm_device_get_device_type: assertion 'NM_IS_DEVICE (self)' failed
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet0): driver 'unknown' does not support carrier detection.
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet0): device is virtual, marking as unmanaged
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet0): new Ethernet device (driver: 'unknown' ifindex: 4)
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet0): exported as /org/freedesktop/NetworkManager/Devices/3
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: nm_device_get_device_type: assertion 'NM_IS_DEVICE (self)' failed
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet1): driver 'unknown' does not support carrier detection.
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet1): device is virtual, marking as unmanaged
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet1): new Ethernet device (driver: 'unknown' ifindex: 5)
Aug 19 18:52:04 n55sf-l NetworkManager[6399]: <info> (vboxnet1): exported as /org/freedesktop/NetworkManager/Devices/4

So, basically it seems that the devices is correctly seen as virtual and unmanaged by Network-Manager but still it finally manages it.

More details obtained using command below confirm that NetworkManager does DHCP on vboxnet0 which is definitely wrong.

grep -i network.*manag.*vbox /var/log/syslog -C 3

Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (wlan0): device state change: unmanaged -> unavailable (reason 'managed') [10 20 2]
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (wlan0): preparing device
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: nm_device_get_device_type: assertion 'NM_IS_DEVICE (self)' failed
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): driver 'unknown' does not support carrier detection.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): device is virtual, marking as unmanaged
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): new Ethernet device (driver: 'unknown' ifindex: 4)
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): exported as /org/freedesktop/NetworkManager/Devices/3
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: nm_device_get_device_type: assertion 'NM_IS_DEVICE (self)' failed
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet1): driver 'unknown' does not support carrier detection.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet1): device is virtual, marking as unmanaged
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet1): new Ethernet device (driver: 'unknown' ifindex: 5)
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet1): exported as /org/freedesktop/NetworkManager/Devices/4
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> urfkill disappeared from the bus
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> use BlueZ version 4
Aug 19 18:59:43 n55sf-l wpa_supplicant[893]: dbus: wpa_dbus_get_object_properties: failed to get object properties: (none) none
--
Aug 19 18:59:43 n55sf-l wpa_supplicant[893]: wlan0: CTRL-EVENT-SCAN-STARTED
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> ModemManager available in the bus
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Auto-activating connection 'Auto SG IP auto'.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) starting connection 'Auto SG IP auto'
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): device state change: unmanaged -> disconnected (reason 'managed') [10 30 2]
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 1 of 5 (Device Prepare) scheduled...
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 1 of 5 (Device Prepare) started...
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): device state change: disconnected -> prepare (reason 'none') [30 40 0]
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> NetworkManager state is now CONNECTING
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 2 of 5 (Device Configure) scheduled...
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 1 of 5 (Device Prepare) complete.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 2 of 5 (Device Configure) starting...
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): device state change: prepare -> config (reason 'none') [40 50 0]
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 2 of 5 (Device Configure) successful.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 3 of 5 (IP Configure Start) scheduled.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 2 of 5 (Device Configure) complete.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 3 of 5 (IP Configure Start) started...
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): device state change: config -> ip-config (reason 'none') [50 70 0]
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Beginning DHCPv4 transaction (timeout in 45 seconds)
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> dhclient started with pid 8181
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> Activation (vboxnet0) Stage 3 of 5 (IP Configure Start) complete.
Aug 19 18:59:43 n55sf-l NetworkManager[8151]: <info> (vboxnet0): DHCPv4 state changed nbi -> preinit
Aug 19 18:59:44 n55sf-l dhclient: DHCPREQUEST of 192.168.56.102 on vboxnet0 to 255.255.255.255 port 67 (xid=0x4b3f5c05)
Aug 19 18:59:44 n55sf-l dhclient: DHCPACK of 192.168.56.102 from 192.168.56.100