Transports that were undocking from the base were trying to stop the fire of the docking point abusing the rules in order to influence the siege result by giving a non-fire window for the cloaked supply ships to enter the base.
Thus they did part took in the battle and were a fair target.
Same as when transport is going off the system under the protection of same rules and passing bots to one of the sides on the way thus influencing the result of the battle. If so = fair target.