We remember this from since 2238, one of BoS quest can't be completed because that one NPC cannot be found at Lost Hills bunker.
Maybe there could be some changes to that bunker quest, or totally remade quest.
You are still initiate, but you can go to Lost Hills and yet there are places that you cannot access inside bunker.
Last quest should be also like other quests before that, you can report to any BoS bunker in towns. After that quest you could get promote and become BoS knight, this would let you go Lost Hills and use all services of bunker.