OK… here is my personal opinion of how to handle this…
AA (or ID as I guess it will be called in this version) represents the BIG guns… the ones with the 20+ k range. Those weapons fire at the SHIPS, the BB’s, DSTs (if applicable) and TRNs.
Those shots should be fired BEFORE units offload (so losign a TRN means losing it scargo also… makes those amphib landings far more risky for the attacker, as they should be.
If you want to add in the net effect of defenders firing at landing craft on their way to the beaches, allow ART (and maybe ARM, but I would limit it to just ART) DEFENDERS to have first strike fire… to attack the amphib forces before they reach shore. That would be only for the very first round of battle, after that ART would be like any other unit (would give ART a defensive purpose other than being over-priced INF on defense).