Can you please share more details about what network settings you would like to modify at runtime, so that I can prove more advice and assistance? Like what type of connection you would like to establish, are there any special settings like static IP addresses, etc. I will answer here to the questions you raise, but it will be really helpful to have more additional context.
Setting DBUS_SYSTEM_BUS_ADDRESS is not enough for multicontainer environment.
You will need to set the following label io.balena.features.dbus: '1'. Setting the dbus label will bind mount the socket path to the container. Without it it won't exist in that location and this is the reason you got the abovenmcli` error.
If you need to use nmcli from an environment then indeed you always have to mask the NetworkManager service installed in the container.
Also please note that possibly you may not need INITSYSTEM set in your container for multicontainer environment. Do you have need any systemd services running in that container? And what are they if yes?
For the device not getting back online after update, can you let us know from which are the two OS versions you are updating from and to. Also how is the device connected to the Internet - Ethernet, WiFi or cellular. And if the connection settings are permanent or they are established each time dynamically from a container.