My solution for the odd sys-net behaviour has been to setup my sys-net to be disposable and to make a simple script that executes when I click a button in my panel. This script tells dom0 to send the Wifi password to the sys-net qube and send the command to it to connect to the Wifi network using the password that it was sent. I also decided to separate my sys-net into two qubes, one for ethernet and one for Wifi, and I made some scripts to quickly set the netvm of my sys-firewall to the sys-net (ethernet) or sys-wifi. This has also allowed me to use the Wifi killswitch whether I have network connected qubes running or not.
To try to keep this simple, below is the simple script to make my sys-wifi connect to one of my Wifi networks:
qvm-run -u root --pass-io sys-wifi 'echo "<PASSWORD>" > b' && sleep 3 && qvm-run -u root --pass-io sys-wifi 'nmcli device wifi connect <NETWORK_SSID> password "$(cat b)"' && rm b