About the Borg Monsters.. Simply remove the Borg Monsters race file from the Race directory and you won't have to worry about them being chosen automatically. Also remove their emp file from the Empires folder as well.
The problem with the Borg Monsters is that they are set up according to how the Monsters are set up in other mods. I do not have a lot of experience with them but will look at the files before the next update and see if I can dumb them down a bit.