At the moment I believe the device (PC, RPi3 etc.) is hanging before restarting, most probably because the network (connmand) or some other vital network-related resource has been shut down too early, which is fairly bad news when booting over the network...
That is exactly the problem. But there is a solution. To circumvent connman to shutdown the interface on reboot/shutdown you need to prevent connman to manage the interface.
Connman has an option to ignore interfaces via a blacklist in its configuration. The configuration is hard coded in squashfs image. But there is a script (/usr/lib/connman/connman-setup) that checks for a custom config before starting connman. Simply copy /etc/connman/main.conf to /storage/.config/connman_main.conf and add the network interface to NetworkInterfaceBlacklist option.