So I wandered into Kingsport lighthouse, killed all the sons of atom and killed the green ghoul at the top of the lighthouse. I put up a settlement beacon and started building things up and scrapping things .. but if I try to use the workbench itself, it says I am not aligned.

From what I read online by killing all the initial inhabitants I should be able to use this. But no luck ..

Any Suggestions? Is there a PC command I can use to fix this?

did you kill the ghoul in the lighthouse

I've not heard of this particular issue...

Do you have an open quest for Kingsport?

maybe a guy fell in the water in that dock hut or someone is stuck in the rocks or like said b4 did you kill the ghoul?

go walk around to see if theres anything there that needs killing & if not, leave, return after respawns & try again?

Yeah, there's
This question really should have been asked in "Cheats, Spoilers and Hints".
Hint hint...

Well I wandered back into this location and got one of the "my friend has been kidnapped" quests ... so took care of that and when I went back and told them, then I got the message I could use the workbench ...

But there's no cheats or spoilers being discussed here? He's just asking why this settlement glitched out. Is it the fact thta settlements exist the "spoiler" you're concerned about? That'd be like saying I "spoiled" the game by saying it's in a post fallout setting...

Yeah, sounds like you just had a little glitch out. I mean if you had set up a beacon and were building and scrapping stuff, you obviously had access to the workbench.