I have the same problem in my game - see "TDM-Modpack politics in really big game"
I started by manually adding the races I wanted without doing an edit on the race. Then as each empire came up I turned on all the ministers and selected players "controlled by computer". If you do it that way not all the race specific files are used, certainly not the one that specifies maximum treaty level. I sent an email to MM but got no reply. Why not send an email yourself ? If enough of us do it, then we may at least get a solid yes or no reply on a bug fix. What is needed is a button in the empires AI selection list to specify use race specific files. Sometimes you might want the default as is, though I can not imagine why.