It sounds like you have just set up the player alliances and relationships wrong for your 'boss'. Instead of using Civilian or Neutral factions for it, try basing it off one of the existing ones and checking in the player template dialog box that it considers everybody else to be enemies and that everybody else considers it an enemy too.
Failing that, or even extra as a safeguard, trigger a script right at the start that overrides the player relationships and makes the boss an enemy to all other players and vice versa.
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