clipping through walls is an issue with game physics so I can try to find a workaround but likely nothing I can do
shooting through walls is another game bug. the line of sight check is from the game and I did not find a better solution for this in the past either
npcs are stationary in the base. I don't believe I can make them move since there is no navmesh there. the game will clip them out of the base if they try to move. I might be able to move them onto a custom navmesh but I don't have time to test this atm
npcs should be alert and attack right away but again it's an issue with the line of sight check not working correctly.
I might be able to implement something where they can open the door, but without the line of sight check working they would just stand there until they get shot. rip
I did report the line of sight issues to Facepunch, described as the CIRCLE PACKING PROBLEM if you are a nerd like me and want to google about it
sorry for lack of solutions but there's not much I can do about those issues.