Once the matchmaking starts, any players that leave the alliance will have a ‘ghost’ team on the battlefield. Since they’re no longer in the alliance they won’t be able to use their flags to hit, but the other alliance can still hit them for points. This does not benefit their alliance.
If a player joins an alliance after matchmaking has started, the player will be put in spectator mode for the war. No team will be placed on the battlefield for them. This does not benefit their alliance.
As for switching out after the war, maybe it’s a family of alliances and they’re moving people around?? Other than that, I can’t think of a strategy that makes sense…