How a cheaper Navy helps the allies is this. The US comes in after turn 4. With a cheaper navy, namely transports, Japan could be a real threat to Australia, forcing the US to pay attention to it, making it historically accurate.
The US paying some attention to Japan helps the Germans.
Lastly, IMHO, the game is close enough that these changes don’t ruin the game. But seeing your point, to go along with this, you would also have to fix the sub problem which is horrible. The advantage Germany had in the beginning of the war with their subs just doesn’t exist in the game. They need to make the subs more stealthy, like rolling the dice to locate them before attacking them, (destroyers would have a better chance than other units) and greatly expanding the areas they can convoy. Also giving the Germans a wolf pack advantage that the US copies and made use of much later in the war against the Japanese.
This whole incredible aspect of WW2 was somehow left out of the game. A real shame. That would bring some balance.