I would lean towards the FCS winning, only because elsewhere we have the "makes more difficult" trumps "makes easier" precedent, but that is a pretty weak connection to say the least.
Leaving aside the strength of the precedent itself (it's very tenuous) I don't think it actually applies in this case.
The FCS is not making a target lock "more difficult" or harder. It's generating a specific operation. There's nothing that locks that operation into an unchanging state. This is the exact same error people were making in the R2/Daredevil discussions. Daredevil didn't change an existent maneuver, it created a new one.
There may be a possible justification for "can't beats can", but I don't think so. The FCS doesn't actually prohibit anything directly. If we had a hypothetical ship that said "Enemy ships may not acquire a target lock on this ship" then ST-321 would be trumped by that. FCS overrides the normal target selection to tell you who you CAN lock - it says nothing about who you CAN'T. So the FCS says "You can lock this target" and ST-321 says "You can lock anyone". Those two don't really conflict.