68 Barracuda Alternator upgrade.

Once you bypass the bulkhead by running the alternator output directly to the battery and put relays for the headlights there's no need to bypass the bulkhead and run the wires in with grommets just make sure the connections are clean and tight and it'll be fine because you don't have the amp draw through it anymore
Ignition, heater fan, wipers, parking lights are all still drawing through the bulkhead connector. And any other extras like that stereo amp may or may not be be drawing power through the feeds depending how its wired in. With what the OP asked about, I would not be so confident that the bulkhead connector terminal is fine. Its all depends on the details.