@matthewgcampbell I have never experienced a scenario where it passes traffic for a short amount of time then stops, at least not in the context of eapol auth related. It either passes or it doesn't. Then again I've never done any proxy bypasses either, can't really comment on odd behavior as a result.
I assume you're following this - https://docs.netgate.com/pfsense/en/latest/recipes/authbridge.html ?
You might want to give a try to one of the proxy scripts here - https://github.com/MonkWho/pfatt/tree/master . This is what we used before vlan0 compliant wpa_supplicant and dhclient.
Edit, one other idea to try is the old dumb switch bypass method.
I can't find a good write up but in essence you connect ethernet from ont and gateway to a dumb switch (preferably not netgear). Wait until the lights on the modem are all green and stop flashing. Disconnect gateway cable while leaving ONT/switch connected. Connect cable from the modem to your pfsense wan port (again, you're not touching the ONT/switch cable). Pfsense should be configured for dhcp on wan.
See if you experience the same disconnect issues after x amount of time. If you do, try a release /renew on the wan. If it doesn't pull an ip, try rebooting pfsense only. This whole time, the link between the ONT and switch should remain connect and as far as ONT concerned, remain authenticated.