Triple A illustrates the transport issue pretty well by having you ‘roll’ for a hit on even an unprotected transport.
Or… it helps to remember a scenario where a larger naval battle is going on and the defenders have 2 or more transports. If the attackers hit enough to kill all defenders and have +1 hit it gets assigned to a transport even if the defenders return enough hits to kill all the attackers so an attacker might kill some but not all transports.