After working with it for a while longer after my first post i eventually got something im ok with. I made my first post while in the middle of solving a problem and was perhaps a little too judgemental of the clipping, Its probably not really any worse than any other shelter its just i knew how to work around the older shelters already and hadn't thought about their problems in a while. The problem with clipping being finicky is still a problem just not a problems unique to that shelter.
As for some statements i made in the comments, i still think the layout is ass, the hallways go nowhere you get two actual rooms and two scaffoldings overlooking the main room that you cant really fit anything on. It was very obviously made with the focus entirely on putting some centerpiece in the main room with little thought given to anything else about its layout. And theres two door frames that aren't filled out by any door, you have to place a doorway in them or use a door with its own wall included.
The esthetic is awesome, the main room could have been cool without the scaffolding and the side rooms could have used more thought, I'm mad about it mostly because it had potential and it was spat on with a lazy awkward layout.
If you like the esthetic of an old bunker then its not the worst thing ever but theres a lot you have to work around but that can be said about a lot with Bethesdas building feature anyway. We shouldn't Have to finick with this to get basic results but we aren't going to get anything better from them 🤷♂️