When you trigger FCS, are you acquiring a target lock? Yes. That meets the requirements for ST-321, and its effect kicks in. That's all there is to it.
I agree so far. ST-321 triggers and you can resolve it. Problem is that "on the defender" is still in effect. You have to resolve "on the defender" as well.
Consider Weapons Engineer: When you acquire a target lock, you may lock onto 2 different ships. Identical trigger, so it activates too, and works. But ST-321 doesn't.
There is one important difference: Weapons engineer overrides the rulebook. There is a rule that cards override the general rules. However, there is no rule that cards override other cards. ST-321 does not override FCS. You need to resolve both. Which you can.