Actually we can skip the 3rd faction thing.
Just allow all non-war-mode players to visit all Alliance / Horde cities and outposts and interact with the NPCs including the flight masters.
As for pro faction divide players who don’t want to see certain races in their cities, I suggest just using different shards for players with and without war mode enabled. This way war mode enabled players will never see players without war mode thus won’t see the “wrong” races in their cities.