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After 50 hours last night I finally built my first settlement item lol, decided that it was getting a complete faff to remove my stockpile of junk before a gun/armour modding session but NOT the rest of my workshop along with it so I decided I would create a steamer trunk beside my workshop and just lump everything that wasn't junk in there so I could simply "Store all junk" and "Take all" from my workshop when it comes to modding sessions.
You don't need to have junk in your inventory to use it for modding. You can leave it in the workshop. You can leave it in any workshop or crafting station in any settlement that is linked to the settlement you are in by provisioning routes, directly or indirectly (e.g. if you have Sanctuary linked to Red Rocket and Red Rocket linked to County Crossing, County Crossing will be linked to Sanctuary).
That's only true for junk - all other items you put in a workbench or crafting station will only be available in that settlement - but you only need it for junk.
I've built a large warehouse style building in Sanctuary that houses the settlement workbench and all of the crafting stations. I also have a lot of containers there:
Unmodified weapons and armour that I intend to mod and distribute to settlers and provisioners.
Modified weapons and armour ready to distribute to settlers and provisioners.
Legendary weapons I'm not using.
Legendary armour I'm not using.
Weapons and armour that I might mod and use myself or which I consider unusual. Gauss rifle, railway rifle, syringer, that sort of thing. Also a lot of Fat Mans.
Power armour pieces.
Alcoholic drinks. I'm building a stock for supplying settlements. Roleplay only, obviously.
General readable items and holotapes.
Recreation items for settlements. Bowling balls and pins, chessboards, pool cues and balls, basketballs, footballs, weights, dumbells, barbells and curling bars...that sort of thing.
In my quarters (which is still just a bed in the original dormitory that was the first building I built), there's a personal trunk for special items. Unique items that aren't useful but have roleplay value, like the "treasures" of Jamaica Plain.
I also keep my magazines in there at the moment because I lost two when I had them in display rack. One of the settlers was hammering at air next to a display rack and dislodged 3 magazines. When I went into the room, I found one of the 3 on the floor but no sign of the other 2.