3) Assumption is the mother of all f***-ups.
I can't say for sure what the bit you're referencing does, but I think it's there so other talents, like Steady Shot, can auto-activate in place of Shoot when not on cooldown. It might have a different function, but's definitely not there to force the actor to start with the Shoot talent. If it did, Temporal Warden probably would not need to have T_SHOOT inside of their birth 'Talents' field.
Anway, it's this bit in Actor.lua inside 'learnTalentPool':
if t.type:find("^technique/archery") then
teaches Shoot automatically.
Since Archer was updated and mastery is no longer split up between bow and sling, technique/archery-bow and technique/archery-sling have been deprecated. Archer gets away with it because they still learn a talent from technique/archery-training or technique/archery-utility. Even with auto-assign talents turned off this will still work for them, because auto-assign is the default and disabling auto-assign actually just takes the points out right after the character is created. So Shoot is learned at birth when they learn a talent from an appropriate category, and it is not un-learned because it's an 'innate' talent.
Just give them Shoot a birth as the easiest way to fix it.
Also, unlike yourself, I gave the poster the benefit of the doubt and took two minutes to try it. Woodsman does not
start with Shoot, regardless of auto-assign. Try it yourself