Spawn zones are manual radius areas that can set any spawn within the zone to team specific, respawn, initial or change them on the fly via a curcumstance, like flag is away or flag is home, etc...
While you can manually set each spawn, you sometimes cannot predict if a spawn setting will work properly in settings like ctf, or other team objectives. It's a delicate balance and you want to present teams with chances of good spawns to keep the gameplay twitchy and interesting.