question on bulkhead connector bypass

That does clear up a few things for me thnks but that does not seem to explain how the VR can reduce charging current to battery when it needs to to prevent overcharging if there is a constant direct charging current to the battery from the alternator via the the starter relay connection.

The VR senses system voltage and varies the field voltage to regulate the alternators output, so just because there is a direct wired connection from the alternator battery stud to the battery doesn't mean it's charging the battery at full output.
How much voltage the field wire (usually green) on the back of the alternator puts into the alternator determines the alternators output.
Normal charging output of the alternator is between 13.8 and 14.2 so you are well within the normal and on the right track to having a nice stable electrical system.

Try running all lighting for the dash, interior and outside lighting besides headlights with LED and watch your electrical systems response.:D
I run with at least my parking lights on to give the charging system something to do besides keep up with the load of an old electrical system with under gauged wiring and the voltage losses from it AND charge the battery.
In return I get headlights that don't dim when idling at a stop light, as well as wipers and blinkers slowing, heater blower and other electricals have all the power they need to always work the same no matter rpm's.

Just saw your last reply.:D
Yes, a relay helps a lot on the sense wire.