Only if custom just means textures. If you add a completely new perk magazine, then wherever you put it in the world, it will be there, as this one only touches the vanilla ones.
I'm on my 5th playthrough, so what difference does it make if I cheat on a Single Player Game? It's not affecting your game, so don't need to come in here and spout that nonsense.
I may be inclined to agree,I may go back in and redo it, without deleting the originals, and just moving them out of playable area, that way, they are still there, in case someone elses mod affects the same space.Time will tell if this is necessary or not.
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http://www.nexusmods.com/fallout4/mods/12490/?