The problem is both SBI and a few players mixing both. They are indeed connected, just the same way other game features/systems are.
In the current iteration a guild can sit together in Caerleon and use the realmgate to be anywhere in the blackzone the moment they have an objective. Any players just logging on to join in on the fight can also log into Caerleon and immediately ride to join the group from the closest portal even if the group has moved substantially. The ability to project power encourages massive groups because it is the most convenient and optimal playstyle which players will naturally gravitate towards.
If an alliance still wants to maintain map wide presence with a new map layout they must split up and keep people in multiple cities (smaller groups), send reinforcements from another city (inconvenient and slow), or have enough alts for every city (inconvenient, large time and monetary investment). Introducing this kind of friction to projecting power will make the groups in fights smaller which can lead to guilds splitting off and doing their own thing.
To keep the convenience of being able to log on and use the local realmgate for content you need to pick one city and a corresponding black zone area to fight in. This means you'll be fighting other people who also decided to stay in that city and opens up the option to relocate to another city to look for smaller groups to fight.