I was baffled, and couldn't find an explanation for it.
EDIT: I found out why.
The adjacency for weapons is determined by a table in lua.scd/lua/sim/adjacencybuffs file. They are listed per pgen type, right? Well, the list used to access them is missing the bonus for structures larger than size4. All I had to do was add them. Now I'm baffled by why I couldn't find this on the internet... I guess I can put this in the vault