RE over rating AA fire of large TFs, well, its a DOS game and there are insufficient resources to do everything. The game has an amazing amount of detail for a DOS game. They went to the max. Back in the old days, a lot of people had to moggie foogie things to free up conventional memory so the game would run.
The undesirable side effect problem applies to flak limits. I've played with flak limits as low as 3250. Problem is, by late in the war, a USN surface combat TF of modern BBs ends up with 4 BBs, 2 CLs, and 8 DDs, not sufficient to encounter an IJN BB TF. So unless the Allied player has already wiped out the IJN BBs he has to avoid surface combat.
In one of my current games, we have a flak limit of 3800. By using TF 56, which undercounts flak, I can get 6 or 7 modern BBs in a TF. That puts it a lot closer to what an IJN TF is likely to have. Allies should not have a severe disadvantage in surface combat due to the flak limit, but certain limitations are unavoidable.
Not to Allied players when there's a flak limit: You have to target IJN BBs early and sink some of them.