You only get the good nights sleep bonus if you have enough beds for every character. How many survivors do you have when you first move before you add a second bunkhouse? My guess is more than 8 but less than 16. The machine shop was there for me and I definitely cleaned out the bedroom area first. My med area is not and can not be upgraded. Thats just how it is/ was. I can tell you that every playthrough I have seen on you tube or done myself has the exact same facilities in the church. Always. I truly think its just an RNG or hard coded and you get what you get but some things are far more likely to happen. For example...I would expect a truck warehouse to have an upgraded garage, and it has in my experience. Just like I would expect a home to have a library of sorts and a dining area. Or a church to have a way to care for the sick. It makes sense.