This is because there is no diplomacy in NCP, so Faction 1 is always the enemy of Faction 2, and there is no 3-factions scenarios.
You can edit gamerules.opt to change that
rulDiplomacyMode = 1
Will activate simple diplomacy. Advanced diplomacy would not work (VGN/PON only).
In Simple Diplomacy, a state of war exists between faction with negative relationships, automatically (and the reverse is true). Having a positive relationship of 25 will mean you share line of sight and supply. You can also have more than 2 factions per scenario.
Hofstadter's Law: "It always takes longer than you expect, even when you take into account Hofstadter's law."