It seems implausible that PC is able to use crafting benches to make weapons, armor etc immediately after leaving the vault. What if you could employ a settler with those skills - in the same way that magazines open new perks, new settlers offer perk buffs?
I'm thinking of the way the overseer in vault 88 interviews settlers. When settlers arrive they ask 'I'm new here, anything I can do to help?' - we should say ' what are you good at?' where they then state the skills they have eg blacksmith, armorer level 2 etc at which point we may accept or reject them as settlers.
Settlers would bring with them any crafting bench they need, make weapons, food, armor & mods on request or for a fee. Crafting then proceeds as previously so no need for new coding other than the bit where benches come with settler attached. (can it be a crafting bench AND a store?)
This is a mash-up of different mods seen on nexus with the addition that PC is no longer able to craft a workbench himself. I would remove most of the existing ones from the game.
For immersion it should be hard to get hold of weapons and ammo 200 years after the bombs so pipe weapons & leathers only. Higher level equipment for BoS and Inst as they have tech so joining their factions should allow better skilled settlers who are then able to produce better equipment.