It happened to me in Pedalu County map also. I quit and made a new game in Pedalu County and same problem. I cheated for an auger and dug down and found the annoying "You are hitting my property" noise so maybe it's spawning under the mountain? I didn't take the time to try and excavate the entire area to confirm that though. The xyz was approx 4, 51, 2. I have re-verified everything and have no mods but I didn't clear the saved game folder in case I decide to revert. I guess the next step is to back that up and try again without it but I'll try a couple other new maps first to see if I have the same problem in them.
Did any of you with this problem notice a bunch of these errors in your logs?
447.841 WRN Could not load prefab 'settlement_trader_04'. Skipping it
447.841 ERR Prefab loading failed. Prefab '' does not exist!