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Sanctuary and Red Rocket both have a full set of Crafting benches when you get to them. I find it strange that the lvl0 (foundation level) scraps them.
Is it possible to leave these be, or maybe move them and incorporate them into the city design at all levels??
Try grabbing the latest version of RotC and Sim Settlements and seeing if a settlement refresh puts them back.
The known alternative workaround is to move the vanilla workbenches slightly before starting the settlement plan. It'll see them as player built and won't touch them in the scrap phase.